1 Reading TE counts

The input files are:

the output tables made by featureCounts (run in rule ‘count_on_TE’ of the Snakefile), which contain read counts of all repetitive elements (i.e. all repNames) for all samples
the repetitive elements annotation ../../data/annotations/RepeatMasker_RepeatLibrary20140131_mm10.noGenes.noSimple.bed (converted to SAF format in rule of Snakefile) used for featureCounts command, that is used to retrieve repFamily and repClass for each repName. The annotation I chose is the most updated library to Nov2020 of rmsk, from which I removed ‘Simple repeats’ and ‘Low complexity regions’
a table with total number of reads per sample in raw fastq files
the samples’ table, containing metadata (i.e. stage)

2 Analysis at family level

2.1 FPKM for each family of Repetitive Elements

For each family of Repetitive Elements (in case of elements with no repFamily name or repFamilies belonging to more than one repClass I use repClass) I compute FPKM values, as follows: for each sample:

I compute the sum of counts for all elements belonging to that repFamily
I divide this sum by the total number of reads for that sample and multiply by 10⁶
I divide this number by the total sum of lengths (in Kb) of the elements belonging to that repFamily –> FPKM
When specified, I subtract from each FPKM the total FPKM of all transposons belonging to the DNA repClass

2.2 Heatmaps

The heatmaps are scaled by rows.

Based on above plots, I remove the early 2-cell sample SRR2927028 and replot.

Note that when correcting for DNA FPKM preimplantation embryonic stages get penalized compared to the oocyte i.e. oocyte FPKM values are overestimated.
The only clear changes emerging above noise from the DNAFPKM-corrected heatmaps are the well-known ERVL upregulation at the late 2-cell stage and ERVL-MaLR upregulation from the zygote to the late 2-cell stage.

3 DE-Seq analysis of RNA transposons between subsequent preimplantation stages

I include the FPKM of DNA repetitive elements as confounding factors in DESeq2 formula.

Before running the Differential Expression analysis, the data are pre-filtered to remove all repetitive elements with < 10 reads among all samples.

I exclude the comparisons with the pre-EGA 2c stage because, after filtering bad samples, this stage includes only one biological replicate.

zygote vs MII oocyte
	baseMean	log2FoldChange	lfcSE	pvalue	padj	repName
MTA_Mm	4718.690175	3.1748847	0.3634000	0.0000000	0.0000000	MTA_Mm
MuLV-int	88.085682	-2.6927603	0.3440952	0.0000000	0.0000000	MuLV-int
ORR1C1-int	111.147533	-2.2180338	0.3099562	0.0000000	0.0000000	ORR1C1-int
MERVL-int	20685.665634	4.9953060	0.6845369	0.0000000	0.0000000	MERVL-int
IAPEY5_I-int	38.248711	-3.2645676	0.4990741	0.0000000	0.0000000	IAPEY5_I-int
L1Lx_I	389.248277	4.1978004	0.6492919	0.0000000	0.0000000	L1Lx_I
L1MdF_III	559.210896	4.5415269	0.7368508	0.0000000	0.0000000	L1MdF_III
IAPEY3-int	83.711688	-2.1674552	0.3871243	0.0000000	0.0000000	IAPEY3-int
L1Lx_IV	449.126064	2.3676198	0.4218458	0.0000000	0.0000000	L1Lx_IV
MTE2b	70.057237	-1.6526674	0.3076528	0.0000000	0.0000000	MTE2b
L1MdF_V	444.474972	4.6627026	0.7802436	0.0000000	0.0000000	L1MdF_V
L1_Mur2	295.244079	2.4685420	0.4784901	0.0000000	0.0000001	L1_Mur2
L1MdF_IV	434.190199	4.5226672	0.8248892	0.0000000	0.0000002	L1MdF_IV
L1MdV_III	323.883563	2.8322766	0.5383078	0.0000000	0.0000002	L1MdV_III
L1MdA_II	620.303707	6.9047750	1.3593773	0.0000000	0.0000002	L1MdA_II
L1MdTf_III	704.552995	6.8377360	1.3522929	0.0000000	0.0000002	L1MdTf_III
L1MdF_I	337.797214	4.4354062	0.8339050	0.0000000	0.0000004	L1MdF_I
L1MdFanc_II	334.287560	6.4520012	1.3521244	0.0000001	0.0000012	L1MdFanc_II
L1MdTf_II	1552.234049	4.4308567	0.8810052	0.0000001	0.0000013	L1MdTf_II
L1MdA_III	614.797032	1.3842525	0.3028999	0.0000001	0.0000017	L1MdA_III
L1MdGf_I	625.823714	2.8070825	0.6065799	0.0000001	0.0000020	L1MdGf_I
L1MdTf_I	1497.502375	6.2833941	1.3696634	0.0000002	0.0000026	L1MdTf_I
L1MdA_VII	258.785943	6.2511344	1.3682401	0.0000002	0.0000028	L1MdA_VII
L1MdFanc_I	399.020299	4.8111655	1.0275653	0.0000003	0.0000044	L1MdFanc_I
MMVL30-int	467.134438	-1.5616339	0.3827172	0.0000005	0.0000072	MMVL30-int
RLTR4_MM-int	291.627871	-1.6920515	0.4230111	0.0000005	0.0000072	RLTR4_MM-int
RLTR11A	35.907051	-1.8214194	0.4595071	0.0000005	0.0000072	RLTR11A
LTR16C	23.156056	-2.0276201	0.5208260	0.0000008	0.0000097	LTR16C
L1MdV_I	317.427103	5.8539656	1.3686398	0.0000008	0.0000099	L1MdV_I
L1MdA_I	806.740430	5.5992849	1.3156553	0.0000010	0.0000125	L1MdA_I
L1MdV_II	189.589619	5.7314517	1.4100466	0.0000018	0.0000213	L1MdV_II
L1MdA_IV	171.565137	5.5694370	1.3844163	0.0000024	0.0000263	L1MdA_IV
L1MdMus_II	249.154096	5.4135279	1.4018126	0.0000043	0.0000463	L1MdMus_II
L1MdF_II	171.072017	5.3764852	1.4103564	0.0000050	0.0000532	L1MdF_II
L1MdA_VI	253.849184	5.0566425	1.3273340	0.0000059	0.0000608	L1MdA_VI
RLTR12G	12.778072	-2.6289203	0.7516829	0.0000072	0.0000721	RLTR12G
RMER19B	447.580477	-0.9497175	0.2453329	0.0000207	0.0002003	RMER19B
L1MdGf_II	250.695268	4.6489404	1.3758842	0.0000220	0.0002074	L1MdGf_II
L1_Mur1	114.598750	2.5380779	0.8132770	0.0000249	0.0002284	L1_Mur1
L1MB5	152.030760	-1.1661879	0.3276026	0.0000266	0.0002377	L1MB5
ORR1C1	37.569853	-1.5714810	0.5029157	0.0000299	0.0002571	ORR1C1
L1_Mur3	370.991728	1.0124855	0.2728160	0.0000302	0.0002571	L1_Mur3
L1MdMus_I	180.467799	4.4710167	1.4203509	0.0000407	0.0003391	L1MdMus_I
B2_Mm1a	1713.375648	3.9889652	1.2838615	0.0000479	0.0003895	B2_Mm1a
L1MdN_I	122.046120	4.6543940	1.5562480	0.0000554	0.0004404	L1MdN_I
MYSERV6-int	168.412775	-0.9264348	0.2562580	0.0000624	0.0004853	MYSERV6-int
RLTR6-int	255.580418	-0.9672811	0.2813070	0.0001025	0.0007807	RLTR6-int
Lx4A	329.849988	-1.0511511	0.3177523	0.0001147	0.0008554	Lx4A
MMETn-int	4901.889603	3.3795022	1.2615548	0.0001365	0.0009973	MMETn-int
Lx	240.763709	1.2671363	0.4577025	0.0002817	0.0020170	Lx
MT2_Mm	2751.765261	3.0644440	1.2901206	0.0002932	0.0020272	MT2_Mm
L1Lx_II	112.641418	2.5592485	1.0870093	0.0002944	0.0020272	L1Lx_II
B2_Mm1t	1112.751367	3.7744599	1.6684367	0.0003542	0.0023923	B2_Mm1t
L1Lx_III	357.830785	1.4049642	0.5507905	0.0003609	0.0023928	L1Lx_III
RMER6C	70.103647	1.3053692	0.4979119	0.0003924	0.0025541	RMER6C
ORR1D2-int	23.826408	1.7437204	0.7503956	0.0004020	0.0025697	ORR1D2-int
MTC-int	215.893874	-0.8820576	0.3043222	0.0008542	0.0053652	MTC-int
MER70A	10.568709	-1.7467171	0.8513966	0.0009626	0.0059414	MER70A
ERVB4_2-I_MM	776.196549	-1.1750603	0.4934774	0.0012526	0.0074244	ERVB4_2-I_MM
MTD-int	49.728075	-0.9377926	0.3473605	0.0012558	0.0074244	MTD-int
L1ME2z	13.146151	-1.5392131	0.7502414	0.0012650	0.0074244	L1ME2z
L1MdA_V	111.829895	2.8574152	1.6304956	0.0014778	0.0085331	L1MdA_V
B2_Mm2	544.932679	2.8981925	1.6992953	0.0016287	0.0092554	B2_Mm2
L1_Rod	96.130374	1.1001317	0.4647249	0.0016992	0.0095049	L1_Rod
MURVY-int	55.737237	3.0431544	1.8755881	0.0018389	0.0101279	MURVY-int
RLTR21	90.609347	-0.9809733	0.4087260	0.0024136	0.0130919	RLTR21
RLTR45	153.507229	2.2024542	1.3559249	0.0025985	0.0137856	RLTR45
RMER21A	17.619506	-1.2219115	0.5963609	0.0026185	0.0137856	RMER21A
RMER13B	45.411250	-1.0467056	0.4649116	0.0027750	0.0143976	RMER13B
B3A	58.354256	2.5486499	1.7290360	0.0032649	0.0166977	B3A
Lx5	315.182188	-0.5514722	0.2069746	0.0039001	0.0196655	Lx5
MMERVK9E_I-int	155.179063	1.3199946	0.7512888	0.0043464	0.0216114	MMERVK9E_I-int
RMER6B	23.061933	-0.9768576	0.4532458	0.0044809	0.0219750	RMER6B
L1MB8	87.922776	-0.8462427	0.3693529	0.0050486	0.0244244	L1MB8
RMER5	97.321057	-0.7670289	0.3247611	0.0053953	0.0257536	RMER5
MuRRS-int	40.156264	2.1673848	1.6754180	0.0062106	0.0292553	MuRRS-int
RLTR13B3	14.216224	2.0812816	1.5936413	0.0063810	0.0296674	RLTR13B3
RLTR19	62.789268	2.1194873	1.6467690	0.0065109	0.0298832	RLTR19
MT2B1	97.873435	0.9800429	0.5016813	0.0070211	0.0314743	MT2B1
Lx6	320.782502	0.5885846	0.2430377	0.0070334	0.0314743	Lx6
L1MA8	14.133320	2.1013243	1.6859431	0.0072481	0.0320348	L1MA8
MuRRS4-int	100.894595	-0.9098673	0.4478121	0.0074680	0.0326043	MuRRS4-int
MTE2b-int	14.996555	-1.0920575	0.6422867	0.0086573	0.0369263	MTE2b-int
L1VL1	28.608534	1.9742705	1.6327623	0.0086643	0.0369263	L1VL1
MLTR11B	22.917514	-0.8903621	0.4691912	0.0106361	0.0447967	MLTR11B
ORR1A3-int	129.841696	-0.7897712	0.4021333	0.0127280	0.0529838	ORR1A3-int
RLTR10-int	690.924548	-0.6495557	0.3156796	0.0150918	0.0616195	RLTR10-int
Lx7	578.885557	-0.5184219	0.2397790	0.0151467	0.0616195	Lx7
Lx3B	79.236226	0.8315281	0.4620531	0.0156987	0.0631475	Lx3B
MLTR18B_MM	9.797181	-1.0278513	0.7135825	0.0175878	0.0699605	MLTR18B_MM
RMER2	32.002247	-0.7554315	0.4077583	0.0178109	0.0700693	RMER2
MusHAL1	22.047186	1.4933456	1.4608135	0.0204519	0.0795845	MusHAL1
ORR1D1	55.642940	0.9234115	0.6219524	0.0214812	0.0826909	ORR1D1
ORR1A4	67.010926	-0.6437520	0.3392411	0.0218253	0.0831217	ORR1A4
IAPLTR1_Mm	89.566333	1.4127874	1.4118202	0.0234567	0.0883948	IAPLTR1_Mm
MERVK26-int	31.205097	-0.7879688	0.4800288	0.0243649	0.0908607	MERVK26-int
RLTR16B_MM	13.310764	-0.8829188	0.6050580	0.0252992	0.0933723	RLTR16B_MM
RMER17A	11.457167	1.3640400	1.4121062	0.0267382	0.0976763	RMER17A
MLT1A0	17.805569	1.2885367	1.2864984	0.0272746	0.0984454	MLT1A0
Lx5b	172.899740	-0.5209681	0.2736171	0.0274987	0.0984454	Lx5b

postEGA 2c vs zygote
	baseMean	log2FoldChange	lfcSE	pvalue	padj	repName
MT2_Mm	2751.765261	7.7193617	0.3699055	0.0000000	0.0000000	MT2_Mm
ORR1A1-int	1900.521786	4.9777258	0.2603529	0.0000000	0.0000000	ORR1A1-int
ORR1A0	232.436518	6.3825652	0.3844886	0.0000000	0.0000000	ORR1A0
ORR1A0-int	3477.346922	6.7457366	0.4195310	0.0000000	0.0000000	ORR1A0-int
MER89	142.145471	6.4620583	0.4522609	0.0000000	0.0000000	MER89
MERVL-int	20685.665634	6.6343849	0.5094547	0.0000000	0.0000000	MERVL-int
ORR1A1	175.556491	4.4024824	0.3548656	0.0000000	0.0000000	ORR1A1
RLTR19	62.789268	4.1033571	0.3428447	0.0000000	0.0000000	RLTR19
MERVL_2A-int	407.117166	4.3973980	0.3767672	0.0000000	0.0000000	MERVL_2A-int
RLTR10C	101.396137	3.4717641	0.3225810	0.0000000	0.0000000	RLTR10C
ORR1A2	142.223361	2.3708493	0.2388593	0.0000000	0.0000000	ORR1A2
MMETn-int	4901.889603	3.5484031	0.3833496	0.0000000	0.0000000	MMETn-int
ORR1A2-int	911.778661	2.4724029	0.2711598	0.0000000	0.0000000	ORR1A2-int
MT2C_Mm	76.176941	3.3189318	0.3782831	0.0000000	0.0000000	MT2C_Mm
RLTR4_Mm	76.552341	3.3942138	0.4073431	0.0000000	0.0000000	RLTR4_Mm
MT2B2	70.389907	2.8958527	0.3587588	0.0000000	0.0000000	MT2B2
ERVB4_2-LTR_MM	87.673552	3.9793603	0.5252278	0.0000000	0.0000000	ERVB4_2-LTR_MM
IAPLTR1_Mm	89.566333	3.1599362	0.4254772	0.0000000	0.0000000	IAPLTR1_Mm
LTRIS_Mus	38.222974	3.1481461	0.4416926	0.0000000	0.0000000	LTRIS_Mus
IAPEY4_I-int	74.817995	3.2864098	0.4717299	0.0000000	0.0000000	IAPEY4_I-int
ORR1A4-int	278.120957	2.5967988	0.3636658	0.0000000	0.0000000	ORR1A4-int
L1MB5	152.030760	-2.1875000	0.3073125	0.0000000	0.0000000	L1MB5
ERVL-B4-int	55.858512	2.7585791	0.4077091	0.0000000	0.0000000	ERVL-B4-int
RMER21B	43.143554	-3.7754388	0.5881516	0.0000000	0.0000000	RMER21B
MT2B	51.983232	2.0765150	0.3097325	0.0000000	0.0000000	MT2B
RMER17A-int	70.638756	-3.0620216	0.4803432	0.0000000	0.0000000	RMER17A-int
MMERVK10C-int	591.716852	1.7569815	0.2682171	0.0000000	0.0000000	MMERVK10C-int
MTC-int	215.893874	-1.9299439	0.2964916	0.0000000	0.0000000	MTC-int
IAPLTR1a_Mm	27.292144	3.4265820	0.5651361	0.0000000	0.0000000	IAPLTR1a_Mm
IAPLTR2_Mm	24.060225	3.0577580	0.4941427	0.0000000	0.0000000	IAPLTR2_Mm
RLTR6_Mm	41.834975	2.4169456	0.4066510	0.0000000	0.0000000	RLTR6_Mm
L1MB8	87.922776	-2.2266665	0.3726048	0.0000000	0.0000000	L1MB8
B2_Mm2	544.932679	2.7043645	0.4741231	0.0000000	0.0000000	B2_Mm2
B2_Mm1t	1112.751367	2.8807462	0.5306140	0.0000000	0.0000001	B2_Mm1t
ORR1A3-int	129.841696	2.1093297	0.3739971	0.0000000	0.0000001	ORR1A3-int
ORR1C1-int	111.147533	-1.6600304	0.2997456	0.0000000	0.0000002	ORR1C1-int
MTB_Mm-int	183.816377	-2.7650885	0.5226629	0.0000000	0.0000002	MTB_Mm-int
B2_Mm1a	1713.375648	2.7607855	0.5384861	0.0000000	0.0000004	B2_Mm1a
IAP-d-int	57.221063	-2.1494864	0.4103743	0.0000000	0.0000006	IAP-d-int
L1MCa	20.478549	-2.2666582	0.4667511	0.0000002	0.0000035	L1MCa
MMERVK9E_I-int	155.179063	1.8069687	0.3724762	0.0000003	0.0000049	MMERVK9E_I-int
B3	175.338095	1.6622156	0.3449026	0.0000004	0.0000057	B3
IAPLTR4	8.099640	3.7361756	0.8910600	0.0000004	0.0000057	IAPLTR4
L1ME2	12.689713	-2.4599788	0.5261182	0.0000004	0.0000059	L1ME2
ERVB7_2B-LTR_MM	9.142095	3.9753927	0.9745082	0.0000004	0.0000064	ERVB7_2B-LTR_MM
B1_Mus2	66.076384	3.5166375	0.8472242	0.0000006	0.0000094	B1_Mus2
LTRIS_Mm	31.286228	3.2596510	0.7766142	0.0000008	0.0000119	LTRIS_Mm
L1MdTf_I	1497.502375	1.4536339	0.3126844	0.0000008	0.0000119	L1MdTf_I
ID_B1	63.485475	1.9812227	0.4359477	0.0000012	0.0000162	ID_B1
IAPLTR2a	8.459672	3.9765554	1.0378493	0.0000013	0.0000170	IAPLTR2a
RLTR10-int	690.924548	-1.4412057	0.3166583	0.0000013	0.0000177	RLTR10-int
RLTRETN_Mm	28.042346	2.1139945	0.4708542	0.0000014	0.0000177	RLTRETN_Mm
RLTR45-int	6971.091058	1.7066816	0.3883356	0.0000026	0.0000336	RLTR45-int
L1MdTf_II	1552.234049	1.4475043	0.3308760	0.0000030	0.0000380	L1MdTf_II
L1M4c	23.603246	-1.9226768	0.4433319	0.0000031	0.0000381	L1M4c
RLTR40	239.861664	-1.8062810	0.4156903	0.0000032	0.0000383	RLTR40
IAPLTR2b	10.243263	2.9157410	0.7241316	0.0000033	0.0000389	IAPLTR2b
MuRRS-int	40.156264	1.8349904	0.4245343	0.0000034	0.0000403	MuRRS-int
ERVB7_1-LTR_MM	32.784875	2.6779510	0.6563760	0.0000039	0.0000450	ERVB7_1-LTR_MM
RLTR9E	55.788276	1.8716033	0.4369807	0.0000040	0.0000454	RLTR9E
RMER6C	70.103647	-1.4584881	0.3396801	0.0000043	0.0000482	RMER6C
RodERV21-int	48.632387	1.6270710	0.3870979	0.0000062	0.0000681	RodERV21-int
MT2B1	97.873435	1.1369595	0.2714846	0.0000075	0.0000809	MT2B1
B3A	58.354256	1.5467552	0.3750539	0.0000089	0.0000943	B3A
L1MB7	56.370275	-1.2518976	0.3032543	0.0000093	0.0000973	L1MB7
RLTR13G	50.979141	3.0646793	0.8372295	0.0000106	0.0001097	RLTR13G
IAP1-MM_I-int	27.432292	1.5872782	0.3929962	0.0000125	0.0001272	IAP1-MM_I-int
L1MdMus_I	180.467799	-1.1332028	0.2786523	0.0000127	0.0001272	L1MdMus_I
L1MD	21.876789	-1.6846347	0.4197971	0.0000135	0.0001320	L1MD
RLTR20B1	21.581115	-2.7104188	0.7226031	0.0000136	0.0001320	RLTR20B1
MLT2B2	10.197537	-3.0709462	0.8559034	0.0000138	0.0001320	MLT2B2
RLTR48A	10.639849	2.6480133	0.7168234	0.0000185	0.0001752	RLTR48A
ORR1D2-int	23.826408	-1.4102901	0.3629866	0.0000246	0.0002289	ORR1D2-int
MTE-int	57.013055	1.3728973	0.3551632	0.0000269	0.0002469	MTE-int
IAPLTR2a2_Mm	19.201928	2.1732129	0.5810329	0.0000284	0.0002573	IAPLTR2a2_Mm
Lx9	334.311664	-0.6741258	0.1685391	0.0000288	0.0002573	Lx9
B1_Mus1	68.244099	2.8698118	0.8274788	0.0000295	0.0002592	B1_Mus1
L1Lx_I	389.248277	-0.6610529	0.1653840	0.0000297	0.0002592	L1Lx_I
B1_Mm	56.581553	2.6847003	0.7915200	0.0000509	0.0004378	B1_Mm
RLTR50B	18.024782	1.8865195	0.5223570	0.0000573	0.0004832	RLTR50B
ORR1A3	26.352387	1.5096331	0.4129661	0.0000582	0.0004832	ORR1A3
ORR1D1-int	29.967482	1.2353840	0.3356134	0.0000583	0.0004832	ORR1D1-int
RSINE1	22.599000	2.7036758	0.8186228	0.0000663	0.0005435	RSINE1
MYSERV-int	29.550454	1.8328741	0.5147663	0.0000712	0.0005763	MYSERV-int
L1M3	21.885271	-1.5484971	0.4326753	0.0000763	0.0006105	L1M3
Lx4A	329.849988	-1.0904571	0.3083194	0.0001089	0.0008612	Lx4A
RLTR6B_Mm	27.211544	1.4621742	0.4254245	0.0001313	0.0010181	RLTR6B_Mm
L1MdV_I	317.427103	-0.9294732	0.2638672	0.0001318	0.0010181	L1MdV_I
L1MA6	34.124975	-1.2868072	0.3763310	0.0001501	0.0011471	L1MA6
RLTR13A3	22.969320	-1.8674081	0.5615297	0.0001561	0.0011794	RLTR13A3
RMER6BA	9.333463	1.9253752	0.5842626	0.0001653	0.0012266	RMER6BA
RLTR21	90.609347	-1.3789489	0.4079956	0.0001660	0.0012266	RLTR21
IAPEY2_LTR	9.759280	2.0898947	0.6572356	0.0002079	0.0015201	IAPEY2_LTR
RLTR14	20.044601	1.4478036	0.4408175	0.0002237	0.0016180	RLTR14
RLTR9D	19.182127	1.5512019	0.4759293	0.0002322	0.0016620	RLTR9D
RMER6A	67.102758	1.0058702	0.3016183	0.0002403	0.0017020	RMER6A
MuLV-int	88.085682	-1.1472229	0.3473926	0.0002431	0.0017041	MuLV-int
RLTR25A	20.925402	1.7063595	0.5322445	0.0002551	0.0017700	RLTR25A
MLT1A1	10.951996	-1.9679752	0.6270959	0.0002633	0.0018086	MLT1A1
L1MdA_I	806.740430	1.2291854	0.3784228	0.0002794	0.0018999	L1MdA_I
MMERGLN-int	490.479182	-1.0103209	0.3105108	0.0003164	0.0021303	MMERGLN-int
MER70A	10.568709	-2.4832167	0.8793237	0.0003735	0.0024901	MER70A
RLTR9A3A	3.842866	3.0658233	1.2494259	0.0004281	0.0028264	RLTR9A3A
L1M2	127.275931	-0.7661368	0.2366499	0.0004329	0.0028305	L1M2
RLTR53_Mm	5.347534	2.3585608	0.8417908	0.0004643	0.0030071	RLTR53_Mm
RLTR13B3	14.216224	-1.6811119	0.5611858	0.0004985	0.0031980	RLTR13B3
RMER20B	19.255719	-1.4510432	0.4812035	0.0005322	0.0033819	RMER20B
MTB_Mm	34.776925	1.4364432	0.4836206	0.0006160	0.0038788	MTB_Mm
MTA_Mm	4718.690175	1.0145653	0.3340189	0.0006399	0.0039920	MTA_Mm
B1_Mur3	9.344677	3.5120816	1.7532240	0.0006461	0.0039943	B1_Mur3
IAPLTR3-int	39.910505	1.4497653	0.4918839	0.0006558	0.0040172	IAPLTR3-int
ERVB2_1A-I_MM	12.412332	-2.0955020	0.7586974	0.0006943	0.0042151	ERVB2_1A-I_MM
RLTR51A_Mm	4.057707	2.4926785	0.9827664	0.0007736	0.0046506	RLTR51A_Mm
MMERVK10D3_I-int	83.817944	1.8109569	0.6441547	0.0007797	0.0046506	MMERVK10D3_I-int
Lx2B2	246.173358	-0.6397944	0.2066974	0.0007994	0.0047268	Lx2B2
MERV1_LTR	8.913517	1.7257383	0.6443597	0.0011991	0.0070293	MERV1_LTR
L1ME3F	1.566199	3.2986723	1.8401927	0.0012291	0.0071435	L1ME3F
MMERVK9C_I-int	274.204475	0.9829116	0.3495946	0.0013033	0.0075108	MMERVK9C_I-int
RLTR1A2_MM	12.240512	1.6612508	0.6267240	0.0013524	0.0077278	RLTR1A2_MM
L1MC1	38.817103	-0.9901287	0.3580734	0.0014830	0.0084021	L1MC1
IAPEY4_LTR	3.125807	3.0614698	1.6447814	0.0014951	0.0084021	IAPEY4_LTR
Lx5c	221.612524	-0.6375640	0.2238295	0.0016529	0.0092127	Lx5c
RLTR17B_Mm	16.373024	1.5194853	0.6028383	0.0021045	0.0116345	RLTR17B_Mm
ETnERV2-int	242.978125	-0.8993827	0.3391150	0.0021976	0.0120514	ETnERV2-int
IAPEz-int	2443.254944	0.9465356	0.3622672	0.0023560	0.0128169	IAPEz-int
L1_Mur2	295.244079	0.5784548	0.2115750	0.0024017	0.0128629	L1_Mur2
RLTR10E	7.493159	1.8874548	0.8018777	0.0024023	0.0128629	RLTR10E
MERV1_I-int	42.109602	-1.1777651	0.4805579	0.0031159	0.0165532	MERV1_I-int
ETnERV3-int	290.412206	-1.1965083	0.4901281	0.0031598	0.0166561	ETnERV3-int
MER34A	4.246620	-2.4139343	1.2633707	0.0033215	0.0173740	MER34A
RLTR9B2	1.686325	2.7209742	1.6848936	0.0035293	0.0183199	RLTR9B2
Lx8	359.831636	-0.6440380	0.2531154	0.0037111	0.0191177	Lx8
L1M4	46.440063	-0.7884608	0.3193254	0.0039496	0.0201586	L1M4
L1MdF_I	337.797214	-0.5672864	0.2229845	0.0039724	0.0201586	L1MdF_I
ERVB7_3-LTR_MM	7.840867	2.0582674	1.0087511	0.0040633	0.0204671	ERVB7_3-LTR_MM
LTR16C	23.156056	-1.0676693	0.4525824	0.0042494	0.0212469	LTR16C
L1MEf	13.510527	-1.3025234	0.5682375	0.0043551	0.0216166	L1MEf
RMER17D2	16.936350	-1.3093767	0.5763485	0.0045656	0.0224972	RMER17D2
L1ME3Cz	3.629116	-2.2652194	1.2356249	0.0046948	0.0229636	L1ME3Cz
RLTR30D2_MM	10.882992	1.7450390	0.8223600	0.0047278	0.0229636	RLTR30D2_MM
L1MdA_VII	258.785943	-0.7763497	0.3241602	0.0048275	0.0232814	L1MdA_VII
IAPEY3C_LTR	5.101940	2.0420099	1.0717432	0.0054650	0.0261706	IAPEY3C_LTR
B1_Mur1	10.020472	2.3783154	1.4854693	0.0059074	0.0279725	B1_Mur1
L1MdV_III	323.883563	0.4535161	0.1881516	0.0059236	0.0279725	L1MdV_III
IAPLTR4_I	5.621351	2.4694167	1.6513340	0.0059716	0.0280047	IAPLTR4_I
L1_Mur3	370.991728	0.4731195	0.1993157	0.0064148	0.0298772	L1_Mur3
MLTR14	33.093030	0.9110044	0.4105953	0.0067630	0.0312848	MLTR14
IAPEY_LTR	9.261945	1.4872925	0.7339628	0.0073319	0.0334798	IAPEY_LTR
RLTR13B2	48.188671	1.4584830	0.7165132	0.0073360	0.0334798	RLTR13B2
ERVB4_2-I_MM	776.196549	-1.0378151	0.4838832	0.0074506	0.0337761	ERVB4_2-I_MM
RLTR20B5_MM	9.118252	-1.4746185	0.7498087	0.0085053	0.0383020	RLTR20B5_MM
RLTR10B2	9.027743	1.3598981	0.6806870	0.0086163	0.0385465	RLTR10B2
RLTR19B	3.302772	2.0554119	1.2550397	0.0088176	0.0391893	RLTR19B
L1MC4a	6.657614	-1.6579863	0.8868458	0.0090002	0.0397413	L1MC4a
ETnERV-int	552.777898	0.8365587	0.3993353	0.0096772	0.0424263	ETnERV-int
Lx10	44.070532	-0.7805668	0.3699961	0.0097331	0.0424263	Lx10
RMER19A	118.271952	-0.5488591	0.2545234	0.0103030	0.0446246	RMER19A
Lx3A	152.629809	-0.9374676	0.4613065	0.0104928	0.0451590	Lx3A
RLTR11D	4.925478	1.4557426	0.7755623	0.0105970	0.0453207	RLTR11D
RMER6-int	10.645472	1.3443339	0.7036958	0.0106951	0.0454541	RMER6-int
RLTR30D_MM	3.452143	1.8105878	1.0723321	0.0110395	0.0466267	RLTR30D_MM
RLTR27	9.768418	1.2473579	0.6496452	0.0111970	0.0469997	RLTR27
L1MdA_V	111.829895	-0.6943378	0.3375100	0.0117669	0.0489303	L1MdA_V
RMER17B2	14.710716	-1.2941914	0.6874066	0.0118274	0.0489303	RMER17B2
L1MdF_IV	434.190199	-0.8551579	0.4266202	0.0118728	0.0489303	L1MdF_IV
MTEa-int	36.291969	1.0172717	0.5202039	0.0119724	0.0489479	MTEa-int
B1_Mur2	6.434517	2.0970028	1.5115889	0.0120210	0.0489479	B1_Mur2
RMER5	97.321057	-0.6655609	0.3274448	0.0127354	0.0515481	RMER5
RMER16A2	4.202485	1.7110054	1.0290523	0.0130362	0.0524533	RMER16A2
RLTR41	19.416434	1.0740416	0.5662581	0.0132781	0.0531123	RLTR41
MLTR18_MM	4.632699	1.7034158	1.0624183	0.0147418	0.0586224	MLTR18_MM
MER34B-int	25.201147	-1.3098341	0.7382332	0.0150044	0.0593198	MER34B-int
MLTR25A	51.795100	0.7072499	0.3678943	0.0160132	0.0626850	MLTR25A
LTR83	2.766397	-1.9432354	1.4440768	0.0160400	0.0626850	LTR83
RLTR30B_MM	2.452236	1.9430092	1.4614100	0.0163646	0.0635882	RLTR30B_MM
RMER2	32.002247	0.7023227	0.3683297	0.0166678	0.0643984	RMER2
RLTR13C3	15.171602	-1.2390046	0.7106059	0.0169678	0.0651870	RLTR13C3
RMER21A	17.619506	0.9251940	0.5054550	0.0171336	0.0654542	RMER21A
ERVB4_1C-LTR_Mm	5.613239	1.5516146	0.9652499	0.0173197	0.0657955	ERVB4_1C-LTR_Mm
ORR1G-int	1.645666	1.9253309	1.5392973	0.0183488	0.0693177	ORR1G-int
MTE2b-int	14.996555	-1.1507720	0.6692390	0.0191042	0.0717726	MTE2b-int
L1MA4A	12.368020	-1.1334302	0.6712906	0.0207735	0.0776151	L1MA4A
IAP1-MM_LTR	2.257144	1.8435575	1.4798375	0.0210633	0.0782680	IAP1-MM_LTR
RLTR31M	8.534716	1.5679322	1.0492559	0.0212125	0.0783941	RLTR31M
L1ME2z	13.146151	-1.1609579	0.7044359	0.0223377	0.0821062	L1ME2z
L1MCc	3.212565	1.8181207	1.5014795	0.0227494	0.0831698	L1MCc
LTR82A	1.501105	-1.8300283	1.6674815	0.0241877	0.0871376	LTR82A
RLTR19-int	81.402293	0.7804087	0.4528910	0.0242645	0.0871376	RLTR19-int
RLTR17C_Mm	1.733294	1.8173586	1.6054944	0.0242928	0.0871376	RLTR17C_Mm
ORR1B1	122.873112	0.5628940	0.3160675	0.0243790	0.0871376	ORR1B1
RLTR9B	3.987524	1.5524730	1.0882572	0.0244754	0.0871376	RLTR9B
B1F2	2.553908	1.7889317	1.5388067	0.0249543	0.0883797	B1F2
RMER17C	18.489050	0.9380834	0.5679374	0.0258245	0.0909877	RMER17C
Lx7	578.885557	-0.4269156	0.2416991	0.0264959	0.0928722	Lx7
RMER13A2	12.492508	-1.0038939	0.6240084	0.0272960	0.0951308	RMER13A2
MTEb	31.164984	0.6725230	0.3955015	0.0274625	0.0951308	MTEb
ORR1F-int	4.590878	1.5278532	1.1097598	0.0275599	0.0951308	ORR1F-int
RMER4A	13.410560	0.9462875	0.5847089	0.0277517	0.0953088	RMER4A
L1M2a	1.357661	-1.7571884	1.6387667	0.0279594	0.0955396	L1M2a
IAPEY5_I-int	38.248711	-0.8597200	0.5303733	0.0292125	0.0989511	IAPEY5_I-int
L1M5	29.049602	-0.7484417	0.4530804	0.0292488	0.0989511	L1M5

4c vs postEGA 2c
	baseMean	log2FoldChange	lfcSE	pvalue	padj	repName
RLTR45-int	6971.091058	3.7982689	0.3788471	0.0000000	0.0000000	RLTR45-int
ERVB4_2-I_MM	776.196549	3.9354747	0.4511096	0.0000000	0.0000000	ERVB4_2-I_MM
RLTR13B1	114.826368	3.2281961	0.4831377	0.0000000	0.0000000	RLTR13B1
L1MdV_I	317.427103	1.7052351	0.2632274	0.0000000	0.0000000	L1MdV_I
RLTR40	239.861664	-2.3047326	0.5528352	0.0000000	0.0000005	RLTR40
MMERVK10C-int	591.716852	1.2680981	0.2567477	0.0000000	0.0000018	MMERVK10C-int
MMETn-int	4901.889603	1.6461648	0.3636484	0.0000000	0.0000018	MMETn-int
Lx5b	172.899740	-1.1597402	0.2577771	0.0000004	0.0000180	Lx5b
L1MdA_II	620.303707	1.0857567	0.2417073	0.0000006	0.0000210	L1MdA_II
L1MB5	152.030760	-1.7033032	0.4499506	0.0000006	0.0000222	L1MB5
L1MdTf_I	1497.502375	1.2397196	0.2944238	0.0000012	0.0000361	L1MdTf_I
ORR1D1-int	29.967482	-1.4800033	0.3949413	0.0000026	0.0000738	ORR1D1-int
L1MdGf_I	625.823714	1.0759973	0.2704345	0.0000055	0.0001460	L1MdGf_I
IAPLTR1_Mm	89.566333	1.1416444	0.2940116	0.0000065	0.0001609	IAPLTR1_Mm
B1_Mus2	66.076384	1.6621129	0.5442685	0.0000113	0.0002600	B1_Mus2
L1MdTf_II	1552.234049	1.1513379	0.3100064	0.0000124	0.0002659	L1MdTf_II
RLTR45	153.507229	1.4152659	0.4532023	0.0000315	0.0006366	RLTR45
B1_Mm	56.581553	1.6255340	0.6176908	0.0000483	0.0009172	B1_Mm
RLTR50B	18.024782	-1.5921703	0.5966050	0.0000507	0.0009172	RLTR50B
RLTR13B2	48.188671	1.4775867	0.5420928	0.0000745	0.0012693	RLTR13B2
Lx3B	79.236226	-1.0434576	0.3141605	0.0000775	0.0012693	Lx3B
MuLV-int	88.085682	1.0495028	0.3336758	0.0001389	0.0021714	MuLV-int
B2_Mm2	544.932679	1.2498989	0.4352508	0.0001458	0.0021813	B2_Mm2
RLTR6B_Mm	27.211544	-1.2106955	0.4320001	0.0002116	0.0030326	RLTR6B_Mm
ETnERV2-int	242.978125	0.9690200	0.3148733	0.0002306	0.0031732	ETnERV2-int
B2_Mm1a	1713.375648	1.2569916	0.4988161	0.0003635	0.0048088	B2_Mm1a
B1_Mus1	68.244099	1.4043920	0.6488254	0.0004078	0.0051961	B1_Mus1
RLTR4_MM-int	291.627871	0.9415244	0.3274280	0.0004850	0.0057353	RLTR4_MM-int
MTE-int	57.013055	-0.9784701	0.3459007	0.0004917	0.0057353	MTE-int
Lx2B2	246.173358	-0.6827324	0.2188274	0.0005002	0.0057353	Lx2B2
B2_Mm1t	1112.751367	1.1564656	0.4777283	0.0007315	0.0080843	B2_Mm1t
Lx9	334.311664	-0.5632913	0.1814255	0.0007520	0.0080843	Lx9
RMER3D-int	72.071743	-1.1095824	0.4794491	0.0011556	0.0120458	RMER3D-int
RMER17A-int	70.638756	-1.2834538	0.7199855	0.0013870	0.0136424	RMER17A-int
RLTR31B2	15.518438	1.0913014	0.4809917	0.0013880	0.0136424	RLTR31B2
ETnERV3-int	290.412206	1.0197536	0.4290414	0.0014621	0.0137905	ETnERV3-int
MTE2b	70.057237	0.7042158	0.2546597	0.0014833	0.0137905	MTE2b
IAPEz-int	2443.254944	0.8312914	0.3231966	0.0017461	0.0158067	IAPEz-int
RLTR13E	18.151547	1.0416543	0.4643488	0.0018255	0.0161016	RLTR13E
Lx7	578.885557	-0.6173394	0.2225350	0.0018800	0.0161676	Lx7
MLT2B1	9.835016	1.1709865	0.6265862	0.0020359	0.0170817	MLT2B1
L1MdA_I	806.740430	0.8386061	0.3380946	0.0021999	0.0180185	L1MdA_I
RLTR13D5	22.784002	-1.1026097	0.5557740	0.0023277	0.0186214	RLTR13D5
RMER19B2	81.220106	-0.7277272	0.2983642	0.0035634	0.0278594	RMER19B2
ORR1D2-int	23.826408	-0.9721821	0.4723027	0.0036526	0.0279221	ORR1D2-int
L1MdTf_III	704.552995	0.5316668	0.2025054	0.0037706	0.0281974	L1MdTf_III
RLTR13A3	22.969320	0.9859998	0.5093229	0.0043436	0.0317917	RLTR13A3
MT2_Mm	2751.765261	-0.7522310	0.3246770	0.0045611	0.0326876	MT2_Mm
MTB_Mm-int	183.816377	-0.9566398	0.4924474	0.0048924	0.0343463	MTB_Mm-int
RLTR13A2	34.274037	0.9877493	0.5450320	0.0052953	0.0364314	RLTR13A2
RLTR13G	50.979141	0.8719719	0.4237557	0.0055264	0.0372764	RLTR13G
L1_Mur3	370.991728	-0.4696906	0.1874709	0.0063000	0.0415102	L1_Mur3
IAPEY2_LTR	9.759280	-0.9874550	0.5884897	0.0063955	0.0415102	IAPEY2_LTR
MTC	116.477847	0.5494742	0.2316232	0.0073398	0.0467569	MTC
L1MdN_I	122.046120	0.7479295	0.3534188	0.0076255	0.0473359	L1MdN_I
Lx8b	170.082455	-0.5344689	0.2255294	0.0077058	0.0473359	Lx8b
Lx3_Mus	216.577970	-0.5557870	0.2374948	0.0078593	0.0474318	Lx3_Mus
L1MdF_I	337.797214	0.5010357	0.2116557	0.0085036	0.0504352	L1MdF_I
L1MA8	14.133320	-0.8611588	0.5219619	0.0121134	0.0706271	L1MA8
L1M2	127.275931	-0.5370950	0.2489961	0.0133067	0.0756890	L1M2
L1MB7	56.370275	-0.6687592	0.3365540	0.0134216	0.0756890	L1MB7
L1MdF_V	444.474972	-0.6343722	0.3146800	0.0140214	0.0773669	L1MdF_V
ETnERV-int	552.777898	0.6564529	0.3314422	0.0141760	0.0773669	ETnERV-int
MYSERV16_I-int	114.323833	-0.7105199	0.3757239	0.0143938	0.0773669	MYSERV16_I-int
MER21C	18.853208	0.7459620	0.4113115	0.0148281	0.0784750	MER21C
RLTR6-int	255.580418	-0.5264734	0.2492418	0.0153132	0.0798142	RLTR6-int
L1MdGf_II	250.695268	0.4592427	0.2115178	0.0158204	0.0812273	L1MdGf_II
ORR1E	67.062404	-0.5691244	0.2841430	0.0176193	0.0879944	ORR1E
MMVL30-int	467.134438	0.5853114	0.2953837	0.0176500	0.0879944	MMVL30-int
MTB-int	163.363455	-0.5950580	0.3091369	0.0194941	0.0944711	MTB-int
RLTR14	20.044601	-0.7066176	0.4044085	0.0194984	0.0944711	RLTR14
MMERVK9C_I-int	274.204475	0.5790517	0.2993829	0.0200386	0.0957397	MMERVK9C_I-int
MERV1_I-int	42.109602	0.7097449	0.4195628	0.0213747	0.0994035	MERV1_I-int
MLT1C2	13.604781	0.7426714	0.4628636	0.0217651	0.0994035	MLT1C2
IAPEY5_I-int	38.248711	-0.8099952	0.6288214	0.0218691	0.0994035	IAPEY5_I-int
RLTR13C2	42.982150	0.7610140	0.4922981	0.0219612	0.0994035	RLTR13C2

8c vs 4c
	baseMean	log2FoldChange	lfcSE	pvalue	padj	repName
ORR1A1-int	1900.52179	-1.3051212	0.2356416	0.0000000	0.0000014	ORR1A1-int
MT2_Mm	2751.76526	-1.5351493	0.3188438	0.0000001	0.0000137	MT2_Mm
MERVL_2A-int	407.11717	-1.5263408	0.3228707	0.0000001	0.0000138	MERVL_2A-int
ORR1A2-int	911.77866	-1.2357528	0.2538978	0.0000002	0.0000138	ORR1A2-int
MTA_Mm	4718.69018	-1.3021702	0.2995038	0.0000013	0.0000905	MTA_Mm
MTB-int	163.36346	-1.3976977	0.3303542	0.0000015	0.0000905	MTB-int
ORR1A0-int	3477.34692	-1.4799727	0.3644767	0.0000021	0.0001086	ORR1A0-int
RLTR19	62.78927	-1.0519783	0.2618174	0.0000071	0.0003161	RLTR19
ERVL-B4-int	55.85851	-1.3607430	0.3694182	0.0000109	0.0004349	ERVL-B4-int
ORR1A0	232.43652	-1.0116554	0.2670929	0.0000159	0.0005530	ORR1A0
MERVL-int	20685.66563	-1.4836103	0.4440670	0.0000170	0.0005530	MERVL-int
ORR1A1	175.55649	-0.9226392	0.3177807	0.0002070	0.0061761	ORR1A1
MTA_Mm-int	52698.16541	-1.2685936	0.5180822	0.0002271	0.0062530	MTA_Mm-int
ETnERV2-int	242.97812	0.9213423	0.3332046	0.0002918	0.0074611	ETnERV2-int
RLTR13B1	114.82637	1.0439464	0.4015150	0.0003540	0.0084487	RLTR13B1
MT-int	1264.50014	-1.1360374	0.5439560	0.0006503	0.0145496	MT-int
IAPEy-int	51.29326	-1.0173407	0.5040597	0.0011280	0.0237544	IAPEy-int
MER89	142.14547	-0.7098314	0.3315788	0.0015529	0.0308853	MER89
ORR1A2	142.22336	-0.5477334	0.2600159	0.0018265	0.0344158	ORR1A2
RLTR13D5	22.78400	0.9657992	0.6006278	0.0022027	0.0373115	RLTR13D5
MTE2b-int	14.99656	-0.9200639	0.7061419	0.0022807	0.0373115	MTE2b-int
RMER21A	17.61951	-0.9219355	0.5249102	0.0022929	0.0373115	RMER21A
Lx5	315.18219	-0.4224663	0.2159796	0.0032362	0.0496516	Lx5
MMERVK9C_I-int	274.20447	0.6671374	0.3628319	0.0033901	0.0496516	MMERVK9C_I-int
MER21C	18.85321	-0.8392735	0.5056225	0.0034673	0.0496516	MER21C
RLTR45	153.50723	0.7867008	0.4739450	0.0040179	0.0553237	RLTR45
Lx2B2	246.17336	-0.4934011	0.2781040	0.0048600	0.0644395	Lx2B2
MTC-int	215.89387	-0.6139037	0.3868811	0.0066852	0.0850852	MTC-int
L1VL1	28.60853	0.7486588	0.5385398	0.0069158	0.0850852	L1VL1
ERVB4_2-I_MM	776.19655	0.6875097	0.4625735	0.0071510	0.0850852	ERVB4_2-I_MM
RLTR10C	101.39614	-0.4796884	0.2944120	0.0073677	0.0850852	RLTR10C
RLTR21	90.60935	-0.6716483	0.4678407	0.0082054	0.0917984	RLTR21
L1MdA_V	111.82989	0.5901619	0.3989626	0.0089737	0.0973515	L1MdA_V

ICM vs 8c
	baseMean	log2FoldChange	lfcSE	pvalue	padj	repName
ORR1A1-int	1900.521786	-3.5395176	0.2492475	0.0000000	0.0000000	ORR1A1-int
L1Lx_I	389.248277	2.0606073	0.1534435	0.0000000	0.0000000	L1Lx_I
MT2_Mm	2751.765261	-4.3824610	0.3495308	0.0000000	0.0000000	MT2_Mm
MTA_Mm	4718.690175	-3.8670612	0.3188344	0.0000000	0.0000000	MTA_Mm
MER89	142.145471	-4.6888688	0.4003604	0.0000000	0.0000000	MER89
ORR1A0	232.436518	-3.6086211	0.3114285	0.0000000	0.0000000	ORR1A0
ORR1A1	175.556491	-3.5313781	0.3455264	0.0000000	0.0000000	ORR1A1
ORR1A2-int	911.778661	-2.6193819	0.2729686	0.0000000	0.0000000	ORR1A2-int
MERVL-int	20685.665634	-4.6115561	0.4820897	0.0000000	0.0000000	MERVL-int
RLTR10C	101.396137	-2.7754855	0.3031859	0.0000000	0.0000000	RLTR10C
MMERVK10C-int	591.716852	-2.3401636	0.2579117	0.0000000	0.0000000	MMERVK10C-int
MTA_Mm-int	52698.165407	-4.6237144	0.5304166	0.0000000	0.0000000	MTA_Mm-int
MT-int	1264.500140	-4.9854033	0.5752170	0.0000000	0.0000000	MT-int
Lx3_Mus	216.577970	1.9854783	0.2279844	0.0000000	0.0000000	Lx3_Mus
L1MdFanc_II	334.287560	1.8840967	0.2161452	0.0000000	0.0000000	L1MdFanc_II
Lx2B2	246.173358	1.8834812	0.2165311	0.0000000	0.0000000	Lx2B2
MT2C_Mm	76.176941	-3.0815274	0.3711341	0.0000000	0.0000000	MT2C_Mm
L1MdF_I	337.797214	1.6279448	0.1968726	0.0000000	0.0000000	L1MdF_I
ORR1A2	142.223361	-1.9219733	0.2378979	0.0000000	0.0000000	ORR1A2
L1MdA_VI	253.849184	1.9906858	0.2507725	0.0000000	0.0000000	L1MdA_VI
B1_Mus2	66.076384	-4.0498448	0.5371313	0.0000000	0.0000000	B1_Mus2
RLTR19	62.789268	-2.6313439	0.3536060	0.0000000	0.0000000	RLTR19
Lx9	334.311664	1.3259854	0.1696278	0.0000000	0.0000000	Lx9
L1MdMus_I	180.467799	1.8734312	0.2447943	0.0000000	0.0000000	L1MdMus_I
B1_Mm	56.581553	-4.5178566	0.6217518	0.0000000	0.0000000	B1_Mm
L1MdGf_II	250.695268	1.4320315	0.1900709	0.0000000	0.0000000	L1MdGf_II
L1MdA_III	614.797032	1.3550822	0.1827875	0.0000000	0.0000000	L1MdA_III
L1MdF_III	559.210896	1.4817156	0.2063725	0.0000000	0.0000000	L1MdF_III
Lx8b	170.082455	1.5747698	0.2217411	0.0000000	0.0000000	Lx8b
B3	175.338095	-2.2411723	0.3285018	0.0000000	0.0000000	B3
MT2B	51.983232	-2.1127019	0.3073681	0.0000000	0.0000000	MT2B
L1_Mur3	370.991728	1.2662199	0.1820418	0.0000000	0.0000000	L1_Mur3
B3A	58.354256	-2.3469133	0.3576281	0.0000000	0.0000000	B3A
B2_Mm2	544.932679	-2.9017851	0.4591171	0.0000000	0.0000000	B2_Mm2
L1MdF_II	171.072017	1.6709937	0.2495339	0.0000000	0.0000000	L1MdF_II
B1_Mus1	68.244099	-4.3265848	0.7016262	0.0000000	0.0000000	B1_Mus1
L1MdF_V	444.474972	2.0973416	0.3265688	0.0000000	0.0000000	L1MdF_V
B4A	113.993403	-1.3535371	0.2024495	0.0000000	0.0000000	B4A
MT2B2	70.389907	-2.2279180	0.3520585	0.0000000	0.0000000	MT2B2
Lx3B	79.236226	1.9890914	0.3123234	0.0000000	0.0000000	Lx3B
ORR1A0-int	3477.346922	-2.4206630	0.3996416	0.0000000	0.0000000	ORR1A0-int
Lx2	359.521136	1.7479560	0.2760717	0.0000000	0.0000000	Lx2
L1_Mur1	114.598750	1.5213693	0.2409094	0.0000000	0.0000000	L1_Mur1
Lx3A	152.629809	2.6660924	0.4583623	0.0000000	0.0000000	Lx3A
L1MdA_V	111.829895	1.7112780	0.2753893	0.0000000	0.0000000	L1MdA_V
ID_B1	63.485475	-2.3998383	0.4139879	0.0000000	0.0000000	ID_B1
Lx	240.763709	1.6576157	0.2788442	0.0000000	0.0000000	Lx
Lx7	578.885557	1.3122040	0.2172301	0.0000000	0.0000000	Lx7
L1_Mur2	295.244079	1.1633621	0.1938800	0.0000000	0.0000000	L1_Mur2
MYSERV16_I-int	114.323833	2.3274489	0.4216472	0.0000000	0.0000000	MYSERV16_I-int
RMER16-int	669.692891	2.2617749	0.4093102	0.0000000	0.0000000	RMER16-int
L1MdTf_III	704.552995	1.1205274	0.1922763	0.0000000	0.0000000	L1MdTf_III
ERVB4_2-LTR_MM	87.673552	-2.1106788	0.3866080	0.0000000	0.0000000	ERVB4_2-LTR_MM
L1MdF_IV	434.190199	2.0963670	0.3847609	0.0000000	0.0000000	L1MdF_IV
Lx5b	172.899740	1.3593257	0.2419239	0.0000000	0.0000001	Lx5b
Lx3C	91.180293	1.3561503	0.2417719	0.0000000	0.0000001	Lx3C
ETnERV-int	552.777898	1.8261194	0.3362802	0.0000000	0.0000001	ETnERV-int
IAPLTR1_Mm	89.566333	-1.6142345	0.2931885	0.0000000	0.0000001	IAPLTR1_Mm
IAPEY4_I-int	74.817995	-2.1191675	0.4057997	0.0000000	0.0000001	IAPEY4_I-int
MURVY-int	55.737237	4.2484846	0.8974412	0.0000000	0.0000001	MURVY-int
ORR1A4-int	278.120957	-1.8118432	0.3397410	0.0000000	0.0000001	ORR1A4-int
L1MdA_IV	171.565137	1.1811798	0.2130834	0.0000000	0.0000001	L1MdA_IV
L1MdV_II	189.589619	1.8473845	0.3656543	0.0000001	0.0000005	L1MdV_II
ORR1A4	67.010926	-1.5738359	0.3085685	0.0000001	0.0000007	ORR1A4
MTEa-int	36.291969	-2.1589091	0.4496706	0.0000001	0.0000008	MTEa-int
L1MdA_VII	258.785943	1.4433396	0.2841917	0.0000001	0.0000010	L1MdA_VII
MT2B1	97.873435	-1.2750301	0.2521665	0.0000002	0.0000014	MT2B1
B2_Mm1t	1112.751367	-2.3068447	0.5026108	0.0000002	0.0000014	B2_Mm1t
LTRIS2	298.700826	2.3127119	0.5071615	0.0000002	0.0000016	LTRIS2
Lx5	315.182188	0.8821726	0.1744880	0.0000003	0.0000022	Lx5
SRV_MM-int	20.273623	-3.5640907	0.8799246	0.0000003	0.0000025	SRV_MM-int
ORR1A3-int	129.841696	-1.7692111	0.3744805	0.0000004	0.0000028	ORR1A3-int
L1MdN_I	122.046120	1.6299691	0.3447672	0.0000005	0.0000037	L1MdN_I
IAPEy-int	51.293256	2.0521903	0.4621460	0.0000007	0.0000053	IAPEy-int
L1M2	127.275931	1.1407101	0.2375646	0.0000008	0.0000057	L1M2
MusHAL1	22.047186	2.2886031	0.5366326	0.0000009	0.0000063	MusHAL1
Lx5c	221.612524	1.0096565	0.2100964	0.0000009	0.0000063	Lx5c
L1Lx_II	112.641418	1.4074983	0.3008861	0.0000010	0.0000068	L1Lx_II
B2_Mm1a	1713.375648	-2.1688056	0.5088694	0.0000012	0.0000084	B2_Mm1a
L1_Rod	96.130374	1.2143067	0.2609491	0.0000014	0.0000100	L1_Rod
RSINE1	22.599000	-2.6420825	0.6820855	0.0000022	0.0000150	RSINE1
RMER19B	447.580477	-1.0401641	0.2256021	0.0000022	0.0000150	RMER19B
B1_Mur4	8.293506	-3.1436417	0.8598970	0.0000025	0.0000167	B1_Mur4
RLTR1B-int	1591.826450	2.1076858	0.5160451	0.0000031	0.0000205	RLTR1B-int
RodERV21-int	48.632387	-1.5216737	0.3524638	0.0000043	0.0000278	RodERV21-int
ORR1B1	122.873112	-1.2241581	0.2846152	0.0000075	0.0000481	ORR1B1
L1MdMus_II	249.154096	0.9448663	0.2177275	0.0000088	0.0000555	L1MdMus_II
Lx6	320.782502	0.8068154	0.1847880	0.0000088	0.0000555	Lx6
MERVL_2A-int	407.117166	-1.4352634	0.3427820	0.0000089	0.0000556	MERVL_2A-int
RLTR30E_MM	28.654635	-1.7626202	0.4383412	0.0000095	0.0000585	RLTR30E_MM
RLTR13B1	114.826368	-1.5267103	0.3699332	0.0000099	0.0000600	RLTR13B1
B1_Mur1	10.020472	-3.7971040	1.2636136	0.0000145	0.0000874	B1_Mur1
Lx2A	20.831817	2.1873947	0.6097150	0.0000201	0.0001195	Lx2A
MLT2B1	9.835016	-2.3389607	0.6703648	0.0000205	0.0001207	MLT2B1
L1MdFanc_I	399.020299	1.0568968	0.2565900	0.0000207	0.0001207	L1MdFanc_I
L1Lx_III	357.830785	1.2956360	0.3219897	0.0000227	0.0001311	L1Lx_III
MTE2a-int	6.231468	4.1447075	1.6016734	0.0000300	0.0001712	MTE2a-int
MMERGLN-int	490.479182	1.1015546	0.2812061	0.0000463	0.0002616	MMERGLN-int
L1MdV_III	323.883563	0.6467083	0.1622869	0.0000533	0.0002984	L1MdV_III
ERVB7_3-LTR_MM	7.840867	2.7355903	0.9272933	0.0000664	0.0003676	ERVB7_3-LTR_MM
Lx2A1	30.744557	1.5603151	0.4313652	0.0000750	0.0004114	Lx2A1
B1_Mur2	6.434517	-3.4778801	1.3808653	0.0000880	0.0004780	B1_Mur2
Lx8	359.831636	0.8818545	0.2324957	0.0000974	0.0005237	Lx8
L1MdV_I	317.427103	0.8127266	0.2200812	0.0001544	0.0008225	L1MdV_I
IAPLTR1a_Mm	27.292144	-1.4354789	0.4143266	0.0001679	0.0008858	IAPLTR1a_Mm
B1_Mur3	9.344677	-2.8516522	1.1100378	0.0001865	0.0009748	B1_Mur3
MTE2b	70.057237	-0.9173887	0.2550041	0.0002033	0.0010524	MTE2b
RLTR4_Mm	76.552341	-1.1117513	0.3149427	0.0002122	0.0010883	RLTR4_Mm
L1MA4	36.721247	1.1321700	0.3216685	0.0002150	0.0010930	L1MA4
RMER19A	118.271952	-0.9384373	0.2654247	0.0002521	0.0012698	RMER19A
RLTR8	8.363612	-2.0973930	0.7203668	0.0002772	0.0013833	RLTR8
IAPLTR2b	10.243263	-1.6426450	0.5178814	0.0003214	0.0015896	IAPLTR2b
L1MA9	15.660769	1.7945056	0.5905037	0.0003630	0.0017799	L1MA9
RLTR14	20.044601	-1.3399209	0.4145695	0.0004537	0.0022050	RLTR14
RMER17D2	16.936350	1.7891733	0.6271154	0.0006652	0.0032044	RMER17D2
ORR1C1-int	111.147533	-0.9900928	0.3047800	0.0006809	0.0032361	ORR1C1-int
B1F	6.367802	-2.4716538	1.0542138	0.0006854	0.0032361	B1F
RLTR26	5.657786	-1.9259813	0.7022862	0.0006893	0.0032361	RLTR26
Lx10	44.070532	1.0401265	0.3231274	0.0007144	0.0033257	Lx10
RLTR10B2	9.027743	-1.6482638	0.5688428	0.0007801	0.0036012	RLTR10B2
Lx4B	126.605343	1.0959127	0.3483509	0.0008596	0.0039359	Lx4B
MTB-int	163.363455	-1.1408903	0.3673795	0.0009318	0.0042315	MTB-int
ERVL-B4-int	55.858512	-1.2681273	0.4215477	0.0010777	0.0048540	ERVL-B4-int
RLTR10E	7.493159	-1.7745601	0.6617786	0.0011500	0.0051380	RLTR10E
MMVL30-int	467.134438	-0.9352537	0.3009328	0.0011707	0.0051885	MMVL30-int
MLT2B2	10.197537	2.6774223	1.4090155	0.0013115	0.0057663	MLT2B2
RLTR10F	8.012838	-1.7542835	0.6659240	0.0013764	0.0060039	RLTR10F
Lx4A	329.849988	0.8855393	0.2889036	0.0014187	0.0061402	Lx4A
MuLV-int	88.085682	-1.0327051	0.3439383	0.0014958	0.0064240	MuLV-int
MT2A	98.008669	-0.7522459	0.2452374	0.0015817	0.0067406	MT2A
RLTR9E	55.788276	-1.1098159	0.3758909	0.0016045	0.0067853	RLTR9E
MTE-int	57.013055	1.0343633	0.3501100	0.0017461	0.0073285	MTE-int
MLTR31D_MM	8.027338	-1.8218335	0.7322792	0.0017921	0.0074648	MLTR31D_MM
MMETn-int	4901.889603	0.9806563	0.3310193	0.0018056	0.0074648	MMETn-int
LTRIS_Mus	38.222974	-0.9749458	0.3302311	0.0018777	0.0077055	LTRIS_Mus
RLTR6_Mm	41.834975	-1.0373516	0.3550454	0.0019325	0.0078720	RLTR6_Mm
RLTR45	153.507229	-1.1570082	0.4072891	0.0021495	0.0086919	RLTR45
MIRb	11.325478	-1.4646106	0.5556034	0.0024390	0.0097912	MIRb
RMER17C-int	36.488428	-1.0890180	0.3864521	0.0025171	0.0100324	RMER17C-int
MLT1F	6.017937	-1.6194685	0.6495169	0.0026966	0.0106707	MLT1F
ORR1D1-int	29.967482	1.0113995	0.3591676	0.0027762	0.0109081	ORR1D1-int
ORR1D2-int	23.826408	1.2898135	0.4851051	0.0030684	0.0119710	ORR1D2-int
IAPEY_LTR	9.261945	-1.4274148	0.5550199	0.0031291	0.0120684	IAPEY_LTR
ORR1A3	26.352387	-1.1339490	0.4158377	0.0031369	0.0120684	ORR1A3
ERVB4_1B-LTR_MM	12.664681	-1.3869487	0.5450964	0.0036255	0.0138518	ERVB4_1B-LTR_MM
RLTRETN_Mm	28.042346	-0.9695243	0.3537131	0.0036569	0.0138761	RLTRETN_Mm
IAPEY4_LTR	3.125807	-2.1427595	1.1551377	0.0040503	0.0152644	IAPEY4_LTR
RLTR42-int	15.418864	-1.1890846	0.4660322	0.0048463	0.0181089	RLTR42-int
IAPLTR3	2.871920	2.2369196	1.3809900	0.0048704	0.0181089	IAPLTR3
MERV1_I-int	42.109602	1.0003293	0.3877159	0.0056798	0.0209774	MERV1_I-int
L1MA6	34.124975	0.9496586	0.3670633	0.0058825	0.0215821	L1MA6
MTB_Mm	34.776925	-1.0050316	0.3937786	0.0061158	0.0222000	MTB_Mm
BGLII	44.143453	1.2014161	0.4883304	0.0061311	0.0222000	BGLII
L1MA5	15.661575	1.1635015	0.4697048	0.0061782	0.0222254	L1MA5
RLTR16B_MM	13.310764	1.4744525	0.6486388	0.0063274	0.0226153	RLTR16B_MM
L1MD3	6.116518	1.9769956	1.1154437	0.0066433	0.0235922	L1MD3
RLTR13D6	64.828745	1.1231293	0.4623054	0.0074321	0.0262254	RLTR13D6
L1ME3	4.256882	2.0343326	1.2561587	0.0075162	0.0263542	L1ME3
RLTR50B	18.024782	-1.3168994	0.5702318	0.0076292	0.0265823	RLTR50B
RLTR13C2	42.982150	-1.2364962	0.5258097	0.0077743	0.0269185	RLTR13C2
RLTR10-int	690.924548	-0.7460627	0.2942641	0.0082472	0.0282371	RLTR10-int
L1Lx_IV	449.126064	0.6711288	0.2626774	0.0082571	0.0282371	L1Lx_IV
B1F2	2.553908	-2.0050378	1.3087092	0.0089534	0.0304306	B1F2
MuRRS4-int	100.894595	-0.9303861	0.3848809	0.0096572	0.0326225	MuRRS4-int
MTE2b-int	14.996555	1.5326224	0.7508892	0.0097430	0.0327130	MTE2b-int
RLTR20B1	21.581115	1.2970400	0.5897607	0.0103681	0.0346019	RLTR20B1
RMER19B2	81.220106	-0.7119927	0.2980845	0.0127363	0.0422511	RMER19B2
ORR1C2-int	19.376334	1.0705497	0.4770880	0.0129304	0.0426396	ORR1C2-int
RMER17A2	19.506885	0.8834607	0.3830652	0.0136264	0.0446687	RMER17A2
RLTR44-int	14.240961	1.1148083	0.5081615	0.0138209	0.0450398	RLTR44-int
ERVB7_2-LTR_MM	5.257771	-1.4943294	0.7874230	0.0142216	0.0460748	ERVB7_2-LTR_MM
ORR1B2	31.177512	-0.7448984	0.3198394	0.0145554	0.0468820	ORR1B2
ORR1D-int	6.911431	1.4515111	0.7689783	0.0157752	0.0505171	ORR1D-int
RLTR1D	8.358817	-1.4648763	0.7871289	0.0162138	0.0516232	RLTR1D
RLTR1B	20.481928	-0.9346101	0.4268261	0.0174065	0.0551041	RLTR1B
RLTR9D	19.182127	-0.9226747	0.4237642	0.0181831	0.0572354	RLTR9D
RMER12	18.965628	0.9470158	0.4400089	0.0188376	0.0589608	RMER12
RLTR13D1	8.441326	1.2578950	0.6423478	0.0192517	0.0599181	RLTR13D1
RMER20B	19.255719	1.0465305	0.5040185	0.0200803	0.0620421	RMER20B
MLT1K	15.846868	-1.0777446	0.5238585	0.0201581	0.0620421	MLT1K
L1MB3	19.792751	0.9793256	0.4651399	0.0203447	0.0622705	L1MB3
L1M4b	10.697815	1.3748311	0.7548920	0.0208110	0.0629765	L1M4b
RMER15	120.195830	-0.7161448	0.3255955	0.0208377	0.0629765	RMER15
ERVB4_1B-I_MM	86.497439	-0.6312648	0.2840034	0.0209164	0.0629765	ERVB4_1B-I_MM
L1MD	21.876789	0.9610094	0.4614400	0.0219480	0.0657252	L1MD
RMER17D	8.150013	1.3839074	0.7766577	0.0220785	0.0657316	RMER17D
RLTR22_Mur	25.690892	0.9132889	0.4348633	0.0221874	0.0657316	RLTR22_Mur
L1MEg	3.428402	1.6432117	1.1538850	0.0226662	0.0667930	L1MEg
IAPLTR3-int	39.910505	0.8843845	0.4216342	0.0230192	0.0674742	IAPLTR3-int
B1F1	1.925961	-1.6768166	1.2904611	0.0234447	0.0683599	B1F1
ERVB7_2B-LTR_MM	9.142095	-1.2026288	0.6333664	0.0239156	0.0690974	ERVB7_2B-LTR_MM
RLTR5_Mm	8.116408	1.4438232	0.8627774	0.0239522	0.0690974	RLTR5_Mm
L2	33.259231	0.8504605	0.4063082	0.0240718	0.0690974	L2
RLTR31M	8.534716	-1.3629637	0.7774297	0.0242421	0.0692276	RLTR31M
HAL1b	3.537146	1.6585172	1.2987957	0.0248283	0.0705379	HAL1b
RLTR13D2	5.374658	1.4468478	0.8815995	0.0251552	0.0711020	RLTR13D2
L2b	7.051410	-1.2003940	0.6408395	0.0253302	0.0712331	L2b
L1M5	29.049602	0.8220643	0.4003992	0.0272348	0.0762023	L1M5
RLTR20D	6.937101	-1.2232830	0.6803048	0.0284411	0.0787639	RLTR20D
MIR	7.606474	-1.2206083	0.6782054	0.0284751	0.0787639	MIR
RMER13B	45.411250	0.8695488	0.4319987	0.0285768	0.0787639	RMER13B
RLTR31B2	15.518438	-0.8996962	0.4574465	0.0307923	0.0844502	RLTR31B2
MMERVK10D3_I-int	83.817944	-1.0249140	0.5499122	0.0333241	0.0909435	MMERVK10D3_I-int
MTC	116.477847	-0.4700324	0.2269812	0.0336907	0.0914935	MTC
RMER16B2	20.433032	0.9802847	0.5257732	0.0352146	0.0951653	RMER16B2
RLTR10	56.905339	-0.6238684	0.3106778	0.0356603	0.0959020	RLTR10
RMER17B	32.558985	0.7823378	0.4017174	0.0361602	0.0967766	RMER17B
RMER16A2	4.202485	-1.2841677	0.8068324	0.0373876	0.0994793	RMER16A2
B4	60.496285	-0.5573272	0.2779638	0.0375292	0.0994793	B4
L1M3	21.885271	0.7153668	0.3660728	0.0377327	0.0995424	L1M3

E3.5 ICM vs 8c
	baseMean	log2FoldChange	lfcSE	pvalue	padj	repName
ORR1A1-int	1900.521786	-3.5178290	0.2723408	0.0000000	0.0000000	ORR1A1-int
L1Lx_I	389.248277	2.0391225	0.1640201	0.0000000	0.0000000	L1Lx_I
MT2_Mm	2751.765261	-4.2664897	0.3812299	0.0000000	0.0000000	MT2_Mm
MTA_Mm	4718.690175	-3.8029050	0.3486596	0.0000000	0.0000000	MTA_Mm
MER89	142.145471	-4.5079849	0.4160186	0.0000000	0.0000000	MER89
ORR1A0	232.436518	-3.6313319	0.3396070	0.0000000	0.0000000	ORR1A0
ORR1A1	175.556491	-3.4649535	0.3759799	0.0000000	0.0000000	ORR1A1
ORR1A2-int	911.778661	-2.6213029	0.2977994	0.0000000	0.0000000	ORR1A2-int
RLTR10C	101.396137	-2.8064775	0.3295448	0.0000000	0.0000000	RLTR10C
MERVL-int	20685.665634	-4.5013863	0.5266428	0.0000000	0.0000000	MERVL-int
MMERVK10C-int	591.716852	-2.3401622	0.2805079	0.0000000	0.0000000	MMERVK10C-int
MTA_Mm-int	52698.165407	-4.5779850	0.5789962	0.0000000	0.0000000	MTA_Mm-int
Lx2B2	246.173358	1.8569914	0.2305755	0.0000000	0.0000000	Lx2B2
L1MdFanc_II	334.287560	1.8633329	0.2322731	0.0000000	0.0000000	L1MdFanc_II
Lx3_Mus	216.577970	1.9288102	0.2432740	0.0000000	0.0000000	Lx3_Mus
MT2C_Mm	76.176941	-3.0213769	0.4020140	0.0000000	0.0000000	MT2C_Mm
MT-int	1264.500140	-4.6882804	0.6265570	0.0000000	0.0000000	MT-int
L1MdF_I	337.797214	1.6256484	0.2116517	0.0000000	0.0000000	L1MdF_I
ORR1A2	142.223361	-1.8893504	0.2557701	0.0000000	0.0000000	ORR1A2
L1MdA_VI	253.849184	1.9530674	0.2691012	0.0000000	0.0000000	L1MdA_VI
RLTR19	62.789268	-2.5944812	0.3733116	0.0000000	0.0000000	RLTR19
L1MdGf_II	250.695268	1.4846776	0.2039187	0.0000000	0.0000000	L1MdGf_II
B1_Mm	56.581553	-4.5969555	0.6861965	0.0000000	0.0000000	B1_Mm
B1_Mus2	66.076384	-3.8935332	0.5898704	0.0000000	0.0000000	B1_Mus2
Lx9	334.311664	1.3042788	0.1815927	0.0000000	0.0000000	Lx9
L1MdMus_I	180.467799	1.8387496	0.2619862	0.0000000	0.0000000	L1MdMus_I
L1MdA_III	614.797032	1.3473939	0.1973259	0.0000000	0.0000000	L1MdA_III
L1MdF_III	559.210896	1.4993155	0.2227151	0.0000000	0.0000000	L1MdF_III
Lx8b	170.082455	1.5568347	0.2364598	0.0000000	0.0000000	Lx8b
MT2B	51.983232	-2.0807214	0.3275341	0.0000000	0.0000000	MT2B
B3A	58.354256	-2.3280099	0.3856720	0.0000000	0.0000000	B3A
L1_Mur3	370.991728	1.2615426	0.1959162	0.0000000	0.0000000	L1_Mur3
B2_Mm2	544.932679	-2.8879895	0.5010827	0.0000000	0.0000000	B2_Mm2
B3	175.338095	-2.1428755	0.3539623	0.0000000	0.0000000	B3
L1MdF_II	171.072017	1.6580791	0.2673911	0.0000000	0.0000000	L1MdF_II
MT2B2	70.389907	-2.2104389	0.3795882	0.0000000	0.0000000	MT2B2
Lx2	359.521136	1.7894020	0.2976784	0.0000000	0.0000000	Lx2
Lx3B	79.236226	1.9348653	0.3291505	0.0000000	0.0000000	Lx3B
L1MdF_V	444.474972	2.0383561	0.3512795	0.0000000	0.0000000	L1MdF_V
B4A	113.993403	-1.3060355	0.2165145	0.0000000	0.0000000	B4A
L1_Mur1	114.598750	1.5323120	0.2571464	0.0000000	0.0000000	L1_Mur1
ORR1A0-int	3477.346922	-2.3872224	0.4326924	0.0000000	0.0000000	ORR1A0-int
B1_Mus1	68.244099	-4.0067330	0.7758277	0.0000000	0.0000000	B1_Mus1
L1MdA_V	111.829895	1.6896584	0.2931193	0.0000000	0.0000000	L1MdA_V
Lx3A	152.629809	2.6092311	0.4907699	0.0000000	0.0000000	Lx3A
Lx7	578.885557	1.3389364	0.2342703	0.0000000	0.0000000	Lx7
ID_B1	63.485475	-2.2959874	0.4439710	0.0000000	0.0000001	ID_B1
L1MdTf_III	704.552995	1.1603405	0.2078811	0.0000000	0.0000001	L1MdTf_III
Lx	240.763709	1.6187524	0.2996981	0.0000000	0.0000002	Lx
RMER16-int	669.692891	2.2240419	0.4401611	0.0000000	0.0000002	RMER16-int
MYSERV16_I-int	114.323833	2.2412071	0.4471078	0.0000000	0.0000002	MYSERV16_I-int
Lx3C	91.180293	1.3695853	0.2569067	0.0000000	0.0000003	Lx3C
L1_Mur2	295.244079	1.1256877	0.2087056	0.0000000	0.0000003	L1_Mur2
L1MdF_IV	434.190199	2.0588972	0.4139248	0.0000000	0.0000005	L1MdF_IV
MURVY-int	55.737237	4.1217372	0.9522746	0.0000001	0.0000006	MURVY-int
ERVB4_2-LTR_MM	87.673552	-2.0188691	0.4151846	0.0000001	0.0000009	ERVB4_2-LTR_MM
L1MdA_IV	171.565137	1.1823250	0.2285838	0.0000001	0.0000010	L1MdA_IV
Lx5b	172.899740	1.3242956	0.2587143	0.0000001	0.0000011	Lx5b
ETnERV-int	552.777898	1.7668292	0.3614202	0.0000002	0.0000015	ETnERV-int
ORR1A4-int	278.120957	-1.7788377	0.3668893	0.0000002	0.0000017	ORR1A4-int
L1MdV_II	189.589619	1.8496904	0.3927928	0.0000003	0.0000028	L1MdV_II
IAPEY4_I-int	74.817995	-1.9939442	0.4336939	0.0000004	0.0000033	IAPEY4_I-int
IAPLTR1_Mm	89.566333	-1.5068674	0.3142656	0.0000005	0.0000038	IAPLTR1_Mm
MTEa-int	36.291969	-2.1701280	0.4872380	0.0000005	0.0000039	MTEa-int
LTRIS2	298.700826	2.3748999	0.5479952	0.0000005	0.0000039	LTRIS2
L1MdN_I	122.046120	1.7275231	0.3706475	0.0000006	0.0000044	L1MdN_I
ORR1A4	67.010926	-1.5463367	0.3300557	0.0000007	0.0000057	ORR1A4
B2_Mm1t	1112.751367	-2.3136734	0.5439191	0.0000008	0.0000064	B2_Mm1t
ORR1A3-int	129.841696	-1.8216720	0.4067937	0.0000011	0.0000082	ORR1A3-int
L1MdA_VII	258.785943	1.4200530	0.3058615	0.0000011	0.0000084	L1MdA_VII
MT2B1	97.873435	-1.2658851	0.2718396	0.0000013	0.0000099	MT2B1
SRV_MM-int	20.273623	-3.3840707	0.9422214	0.0000021	0.0000154	SRV_MM-int
B2_Mm1a	1713.375648	-2.2499205	0.5532615	0.0000023	0.0000163	B2_Mm1a
Lx5	315.182188	0.8600730	0.1874313	0.0000030	0.0000211	Lx5
MusHAL1	22.047186	2.1998939	0.5548825	0.0000040	0.0000281	MusHAL1
L1M2	127.275931	1.1299696	0.2532558	0.0000041	0.0000281	L1M2
L1_Rod	96.130374	1.2281124	0.2781995	0.0000044	0.0000303	L1_Rod
IAPEy-int	51.293256	1.9695251	0.4869556	0.0000052	0.0000353	IAPEy-int
L1Lx_II	112.641418	1.3753002	0.3220572	0.0000069	0.0000458	L1Lx_II
Lx5c	221.612524	0.9786155	0.2255852	0.0000085	0.0000561	Lx5c
B1_Mur4	8.293506	-3.0531129	0.9164994	0.0000088	0.0000571	B1_Mur4
RLTR1B-int	1591.826450	2.0662416	0.5536854	0.0000150	0.0000963	RLTR1B-int
L1MdMus_II	249.154096	0.9786783	0.2344095	0.0000177	0.0001122	L1MdMus_II
RSINE1	22.599000	-2.4361119	0.7098929	0.0000193	0.0001211	RSINE1
RLTR13B1	114.826368	-1.5689435	0.3998781	0.0000218	0.0001347	RLTR13B1
L1Lx_III	357.830785	1.3841811	0.3475282	0.0000237	0.0001447	L1Lx_III
RMER19B	447.580477	-0.9907178	0.2437391	0.0000283	0.0001708	RMER19B
RodERV21-int	48.632387	-1.4736278	0.3778012	0.0000286	0.0001711	RodERV21-int
RLTR30E_MM	28.654635	-1.7280148	0.4588454	0.0000297	0.0001754	RLTR30E_MM
ORR1B1	122.873112	-1.2183689	0.3072349	0.0000327	0.0001908	ORR1B1
MTE2a-int	6.231468	4.0570220	1.6439004	0.0000378	0.0002187	MTE2a-int
B1_Mur1	10.020472	-3.3856394	1.2231002	0.0000410	0.0002346	B1_Mur1
Lx2A	20.831817	2.1412348	0.6363691	0.0000509	0.0002879	Lx2A
Lx6	320.782502	0.7851106	0.1990245	0.0000569	0.0003148	Lx6
L1MdFanc_I	399.020299	1.0730749	0.2769390	0.0000572	0.0003148	L1MdFanc_I
MLT2B1	9.835016	-2.3086704	0.7172580	0.0000575	0.0003148	MLT2B1
ERVB7_3-LTR_MM	7.840867	2.7092998	0.9505344	0.0000876	0.0004750	ERVB7_3-LTR_MM
MERVL_2A-int	407.117166	-1.3381427	0.3685351	0.0001056	0.0005667	MERVL_2A-int
L1MdV_III	323.883563	0.6548565	0.1747655	0.0001408	0.0007481	L1MdV_III
B1_Mur2	6.434517	-3.2085369	1.4177900	0.0002156	0.0011341	B1_Mur2
Lx2A1	30.744557	1.5046312	0.4540512	0.0002577	0.0013418	Lx2A1
B1_Mur3	9.344677	-2.9148935	1.2404070	0.0002774	0.0014307	B1_Mur3
MTE2b	70.057237	-0.9317690	0.2712959	0.0003710	0.0018948	MTE2b
Lx8	359.831636	0.8579224	0.2507025	0.0004166	0.0021072	Lx8
RLTR4_Mm	76.552341	-1.1238173	0.3399961	0.0004780	0.0023944	RLTR4_Mm
RLTR8	8.363612	-2.0567130	0.7478048	0.0004873	0.0024182	RLTR8
L1MA9	15.660769	1.8006483	0.6137538	0.0004993	0.0024544	L1MA9
L1MA4	36.721247	1.1076762	0.3386001	0.0005502	0.0026795	L1MA4
MMERGLN-int	490.479182	0.9966950	0.3031413	0.0005897	0.0028457	MMERGLN-int
RLTR14	20.044601	-1.3800923	0.4420092	0.0006214	0.0029672	RLTR14
L1MdV_I	317.427103	0.7896396	0.2373957	0.0006262	0.0029672	L1MdV_I
RMER19A	118.271952	-0.9175612	0.2832962	0.0007604	0.0035711	RMER19A
IAPLTR1a_Mm	27.292144	-1.3442243	0.4374062	0.0007764	0.0036142	IAPLTR1a_Mm
Lx4B	126.605343	1.1656129	0.3740177	0.0008720	0.0040233	Lx4B
IAPLTR2b	10.243263	-1.5582662	0.5376387	0.0009313	0.0042598	IAPLTR2b
ORR1C1-int	111.147533	-1.0226519	0.3254581	0.0009512	0.0043131	ORR1C1-int
RLTR26	5.657786	-1.9486275	0.7500934	0.0009758	0.0043867	RLTR26
RMER17D2	16.936350	1.7447657	0.6462078	0.0011503	0.0051275	RMER17D2
RLTR10E	7.493159	-1.7970144	0.7015179	0.0015193	0.0067156	RLTR10E
MLT2B2	10.197537	2.5826175	1.4015582	0.0015623	0.0068481	MLT2B2
B1F	6.367802	-2.1211234	0.9826007	0.0020772	0.0089627	B1F
MTE-int	57.013055	1.0729755	0.3717625	0.0020788	0.0089627	MTE-int
Lx10	44.070532	0.9812092	0.3420192	0.0024375	0.0104238	Lx10
RLTR10B2	9.027743	-1.5086871	0.5851153	0.0026420	0.0112074	RLTR10B2
MLTR31D_MM	8.027338	-1.8035793	0.7787602	0.0028574	0.0120239	MLTR31D_MM
ERVL-B4-int	55.858512	-1.2153892	0.4476055	0.0029103	0.0121492	ERVL-B4-int
ORR1A3	26.352387	-1.1888036	0.4449445	0.0034365	0.0142330	ORR1A3
MMVL30-int	467.134438	-0.8982078	0.3249494	0.0036721	0.0150901	MMVL30-int
MMETn-int	4901.889603	0.9741752	0.3569969	0.0037807	0.0154159	MMETn-int
MTB-int	163.363455	-1.0496166	0.3901637	0.0038960	0.0157637	MTB-int
BGLII	44.143453	1.3124010	0.5152926	0.0040791	0.0163786	BGLII
MIRb	11.325478	-1.4413996	0.5865636	0.0041711	0.0166214	MIRb
RMER17C-int	36.488428	-1.0949697	0.4146410	0.0042626	0.0168582	RMER17C-int
ORR1D2-int	23.826408	1.2735680	0.4998483	0.0043255	0.0169791	ORR1D2-int
RLTRETN_Mm	28.042346	-1.0106940	0.3790608	0.0043745	0.0170444	RLTRETN_Mm
L1MD3	6.116518	2.0742173	1.1502962	0.0048003	0.0185658	L1MD3
Lx4A	329.849988	0.8361272	0.3107324	0.0048572	0.0186487	Lx4A
MERV1_I-int	42.109602	1.0689225	0.4125635	0.0050855	0.0192616	MERV1_I-int
RLTR10F	8.012838	-1.5406708	0.6678830	0.0050900	0.0192616	RLTR10F
IAPLTR3	2.871920	2.1762821	1.3801288	0.0053439	0.0200778	IAPLTR3
RLTR45	153.507229	-1.1146306	0.4375052	0.0054283	0.0202504	RLTR45
ERVB4_1B-LTR_MM	12.664681	-1.3579649	0.5764402	0.0063150	0.0233920	ERVB4_1B-LTR_MM
IAPEY4_LTR	3.125807	-1.9909638	1.1451122	0.0064230	0.0236260	IAPEY4_LTR
MT2A	98.008669	-0.6873808	0.2618769	0.0066678	0.0243559	MT2A
RLTR16B_MM	13.310764	1.4954530	0.6711241	0.0067418	0.0244564	RLTR16B_MM
MLT1F	6.017937	-1.4881148	0.6699818	0.0069570	0.0249748	MLT1F
ORR1D1-int	29.967482	0.9524968	0.3771790	0.0070039	0.0249748	ORR1D1-int
L1MA5	15.661575	1.1837885	0.4892607	0.0070271	0.0249748	L1MA5
RLTR9E	55.788276	-1.0052358	0.4021473	0.0070995	0.0250628	RLTR9E
LTRIS_Mus	38.222974	-0.8805610	0.3506411	0.0078407	0.0274948	LTRIS_Mus
L1ME3	4.256882	1.9570236	1.2578810	0.0090049	0.0313681	L1ME3
MuLV-int	88.085682	-0.8820812	0.3602637	0.0093252	0.0322700	MuLV-int
IAPEY_LTR	9.261945	-1.2810238	0.5737147	0.0097905	0.0336589	IAPEY_LTR
RLTR6_Mm	41.834975	-0.9059262	0.3753123	0.0100104	0.0341914	RLTR6_Mm
L1MA6	34.124975	0.9261443	0.3854954	0.0101092	0.0343061	L1MA6
MuRRS4-int	100.894595	-0.9799590	0.4152751	0.0106909	0.0360476	MuRRS4-int
MTB_Mm	34.776925	-0.9829306	0.4213366	0.0114394	0.0383257	MTB_Mm
RLTR50B	18.024782	-1.2725413	0.5975704	0.0127284	0.0423742	RLTR50B
RLTR42-int	15.418864	-1.0942265	0.4910849	0.0130517	0.0431773	RLTR42-int
L1Lx_IV	449.126064	0.6748048	0.2836696	0.0134540	0.0442300	L1Lx_IV
B1F2	2.553908	-1.8454122	1.3179155	0.0136009	0.0444351	B1F2
RLTR44-int	14.240961	1.1316349	0.5288543	0.0154016	0.0500077	RLTR44-int
RMER12	18.965628	1.0035005	0.4601148	0.0164545	0.0530986	RMER12
MTE2b-int	14.996555	1.4315978	0.7644104	0.0166826	0.0535064	MTE2b-int
RLTR13C2	42.982150	-1.1443188	0.5601152	0.0189801	0.0601323	RLTR13C2
MLT1K	15.846868	-1.1417695	0.5584576	0.0189852	0.0601323	MLT1K
L2b	7.051410	-1.3222698	0.6940958	0.0191946	0.0601323	L2b
RMER17A2	19.506885	0.8754003	0.4024188	0.0192058	0.0601323	RMER17A2
RLTR13D1	8.441326	1.2866803	0.6663679	0.0193637	0.0602679	RLTR13D1
ERVB7_2-LTR_MM	5.257771	-1.4329065	0.8123939	0.0204879	0.0633920	ERVB7_2-LTR_MM
ERVB7_2B-LTR_MM	9.142095	-1.2887524	0.6794320	0.0207186	0.0637309	ERVB7_2B-LTR_MM
RLTR13D6	64.828745	1.0150135	0.4910625	0.0213662	0.0651045	RLTR13D6
ORR1C2-int	19.376334	1.0320639	0.5018457	0.0214334	0.0651045	ORR1C2-int
L1MEg	3.428402	1.6480746	1.1658760	0.0215365	0.0651045	L1MEg
L2	33.259231	0.9069159	0.4293624	0.0217088	0.0652506	L2
RLTR20B1	21.581115	1.1862990	0.6147917	0.0229167	0.0684898	RLTR20B1
HAL1b	3.537146	1.6545944	1.3066273	0.0235938	0.0701150	HAL1b
L1M5	29.049602	0.8840044	0.4242267	0.0238141	0.0703719	L1M5
ORR1B2	31.177512	-0.7238993	0.3381621	0.0240064	0.0705438	ORR1B2
RLTR10-int	690.924548	-0.6828320	0.3175315	0.0241964	0.0707072	RLTR10-int
RLTR13D2	5.374658	1.4597691	0.9089041	0.0253772	0.0737480	RLTR13D2
L1MD	21.876789	0.9669377	0.4797020	0.0255191	0.0737529	L1MD
RLTR1B	20.481928	-0.9205802	0.4554209	0.0265473	0.0763052	RLTR1B
RLTR1D	8.358817	-1.3727610	0.8220227	0.0272718	0.0779618	RLTR1D
RLTR9D	19.182127	-0.8785116	0.4483064	0.0320224	0.0910476	RLTR9D
RMER20B	19.255719	0.9847395	0.5230743	0.0336639	0.0952002	RMER20B
L1M4b	10.697815	1.2730785	0.7705313	0.0340225	0.0956997	L1M4b
RLTR22_Mur	25.690892	0.8857953	0.4621380	0.0350041	0.0976096	RLTR22_Mur
RLTR45-int	6971.091058	-0.7420470	0.3754960	0.0350843	0.0976096	RLTR45-int
RMER17D	8.150013	1.2951003	0.8058209	0.0352582	0.0976096	RMER17D
MMERVK10D3_I-int	83.817944	-1.0647859	0.5895318	0.0355923	0.0980187	MMERVK10D3_I-int
L1MB3	19.792751	0.9242800	0.4910957	0.0362173	0.0992204	L1MB3
RLTR20D	6.937101	-1.2068078	0.7187910	0.0365035	0.0994861	RLTR20D

E3.5 TE vs 8c
	baseMean	log2FoldChange	lfcSE	pvalue	padj	repName
ORR1A1-int	1900.521786	-4.7041095	0.2825015	0.0000000	0.0000000	ORR1A1-int
L1Lx_I	389.248277	2.2106431	0.1669066	0.0000000	0.0000000	L1Lx_I
MT2_Mm	2751.765261	-4.5328530	0.3902952	0.0000000	0.0000000	MT2_Mm
ORR1A0	232.436518	-3.7150916	0.3456127	0.0000000	0.0000000	ORR1A0
MTA_Mm	4718.690175	-3.5305894	0.3554559	0.0000000	0.0000000	MTA_Mm
MER89	142.145471	-3.9533340	0.3979268	0.0000000	0.0000000	MER89
ORR1A2-int	911.778661	-2.8323430	0.3030726	0.0000000	0.0000000	ORR1A2-int
ORR1A0-int	3477.346922	-3.9523085	0.4428751	0.0000000	0.0000000	ORR1A0-int
MERVL-int	20685.665634	-4.7420982	0.5353733	0.0000000	0.0000000	MERVL-int
Lx3_Mus	216.577970	2.2089174	0.2485603	0.0000000	0.0000000	Lx3_Mus
ORR1A1	175.556491	-3.2537523	0.3753098	0.0000000	0.0000000	ORR1A1
L1MdF_I	337.797214	1.8831250	0.2168909	0.0000000	0.0000000	L1MdF_I
L1MdFanc_II	334.287560	2.0406685	0.2376803	0.0000000	0.0000000	L1MdFanc_II
Lx9	334.311664	1.5569483	0.1849953	0.0000000	0.0000000	Lx9
RLTR10C	101.396137	-2.6174756	0.3261872	0.0000000	0.0000000	RLTR10C
MT2C_Mm	76.176941	-3.2520200	0.4150476	0.0000000	0.0000000	MT2C_Mm
RLTR19	62.789268	-3.1928626	0.4168856	0.0000000	0.0000000	RLTR19
Lx2B2	246.173358	1.8607099	0.2346220	0.0000000	0.0000000	Lx2B2
MMERVK10C-int	591.716852	-2.1672468	0.2833196	0.0000000	0.0000000	MMERVK10C-int
L1MdMus_I	180.467799	2.0184685	0.2683236	0.0000000	0.0000000	L1MdMus_I
L1MdA_VI	253.849184	2.0656579	0.2756408	0.0000000	0.0000000	L1MdA_VI
MT2B2	70.389907	-2.9287072	0.4191259	0.0000000	0.0000000	MT2B2
L1MdA_III	614.797032	1.4842242	0.2020152	0.0000000	0.0000000	L1MdA_III
L1MdGf_II	250.695268	1.4853227	0.2088434	0.0000000	0.0000000	L1MdGf_II
RLTR13B1	114.826368	-2.9641667	0.4454218	0.0000000	0.0000000	RLTR13B1
MT-int	1264.500140	-4.2285488	0.6445132	0.0000000	0.0000000	MT-int
Lx2	359.521136	2.1093067	0.3067504	0.0000000	0.0000000	Lx2
B2_Mm2	544.932679	-3.3196940	0.5047690	0.0000000	0.0000000	B2_Mm2
Lx8b	170.082455	1.6784836	0.2413037	0.0000000	0.0000000	Lx8b
B1_Mus2	66.076384	-3.8768691	0.5983954	0.0000000	0.0000000	B1_Mus2
Lx3B	79.236226	2.2230164	0.3364157	0.0000000	0.0000000	Lx3B
L1MdF_II	171.072017	1.8472726	0.2744550	0.0000000	0.0000000	L1MdF_II
MT2B	51.983232	-2.2560655	0.3441917	0.0000000	0.0000000	MT2B
ORR1A2	142.223361	-1.7343918	0.2594939	0.0000000	0.0000000	ORR1A2
L1MdF_V	444.474972	2.3158251	0.3618501	0.0000000	0.0000000	L1MdF_V
ORR1A4-int	278.120957	-2.4701715	0.3897836	0.0000000	0.0000000	ORR1A4-int
B1_Mus1	68.244099	-4.7424143	0.8018094	0.0000000	0.0000000	B1_Mus1
L1MdF_III	559.210896	1.4740118	0.2279368	0.0000000	0.0000000	L1MdF_III
B3	175.338095	-2.2631911	0.3647786	0.0000000	0.0000000	B3
B1_Mm	56.581553	-4.0246794	0.6856202	0.0000000	0.0000000	B1_Mm
RLTR45-int	6971.091058	-2.4753742	0.4076246	0.0000000	0.0000000	RLTR45-int
MTA_Mm-int	52698.165407	-3.4818988	0.6058587	0.0000000	0.0000000	MTA_Mm-int
L1_Mur3	370.991728	1.2695574	0.2000576	0.0000000	0.0000000	L1_Mur3
MMETn-int	4901.889603	-2.3094480	0.3845340	0.0000000	0.0000000	MMETn-int
ERVB4_2-I_MM	776.196549	-2.6686095	0.4770709	0.0000000	0.0000000	ERVB4_2-I_MM
ERVB4_2-LTR_MM	87.673552	-2.4929140	0.4428023	0.0000000	0.0000000	ERVB4_2-LTR_MM
Lx5	315.182188	1.1501193	0.1909587	0.0000000	0.0000000	Lx5
L1_Mur2	295.244079	1.2701308	0.2131474	0.0000000	0.0000000	L1_Mur2
Lx3A	152.629809	2.7141449	0.4953390	0.0000000	0.0000000	Lx3A
B4A	113.993403	-1.2966173	0.2244244	0.0000000	0.0000000	B4A
Lx	240.763709	1.7305038	0.3073998	0.0000000	0.0000000	Lx
RLTR45	153.507229	-2.6087773	0.4920394	0.0000000	0.0000000	RLTR45
MURVY-int	55.737237	4.5581115	0.9202634	0.0000000	0.0000000	MURVY-int
B3A	58.354256	-2.1018502	0.3855994	0.0000000	0.0000000	B3A
Lx3C	91.180293	1.4855255	0.2630932	0.0000000	0.0000000	Lx3C
L1MdF_IV	434.190199	2.2330993	0.4258222	0.0000000	0.0000001	L1MdF_IV
B2_Mm1t	1112.751367	-2.7849636	0.5637975	0.0000000	0.0000002	B2_Mm1t
L1_Mur1	114.598750	1.4267958	0.2630771	0.0000000	0.0000002	L1_Mur1
L1MdA_IV	171.565137	1.2705825	0.2338099	0.0000000	0.0000002	L1MdA_IV
L1MdA_VII	258.785943	1.6417941	0.3148670	0.0000000	0.0000004	L1MdA_VII
B2_Mm1a	1713.375648	-2.6834332	0.5746331	0.0000001	0.0000007	B2_Mm1a
RLTR9E	55.788276	-2.2290553	0.4620750	0.0000001	0.0000008	RLTR9E
L1MdA_V	111.829895	1.5208681	0.3006539	0.0000001	0.0000010	L1MdA_V
ETnERV2-int	242.978125	-1.6549168	0.3323963	0.0000002	0.0000012	ETnERV2-int
RLTRETN_Mm	28.042346	-2.1748117	0.4571150	0.0000002	0.0000012	RLTRETN_Mm
ID_B1	63.485475	-2.1047601	0.4449402	0.0000002	0.0000016	ID_B1
RLTR30E_MM	28.654635	-2.4632586	0.5381099	0.0000002	0.0000016	RLTR30E_MM
L1MdV_II	189.589619	1.9041019	0.4027649	0.0000003	0.0000025	L1MdV_II
IAPEy-int	51.293256	2.2877452	0.5036253	0.0000004	0.0000027	IAPEy-int
Lx5b	172.899740	1.2859576	0.2651542	0.0000005	0.0000038	Lx5b
MusHAL1	22.047186	2.4696850	0.5669923	0.0000006	0.0000043	MusHAL1
IAPEY4_I-int	74.817995	-2.0121319	0.4429220	0.0000007	0.0000046	IAPEY4_I-int
Lx5c	221.612524	1.1112339	0.2303182	0.0000007	0.0000051	Lx5c
ORR1A3-int	129.841696	-1.9103234	0.4202233	0.0000008	0.0000054	ORR1A3-int
L1Lx_II	112.641418	1.5289708	0.3311179	0.0000012	0.0000077	L1Lx_II
L1_Rod	96.130374	1.3252522	0.2846510	0.0000013	0.0000086	L1_Rod
B1_Mur4	8.293506	-3.7441863	1.0165520	0.0000019	0.0000125	B1_Mur4
MMERVK9C_I-int	274.204475	-1.4874937	0.3374298	0.0000033	0.0000214	MMERVK9C_I-int
RMER16B2	20.433032	2.4157812	0.6063598	0.0000037	0.0000230	RMER16B2
RMER19B	447.580477	-1.1011766	0.2504483	0.0000059	0.0000370	RMER19B
Lx6	320.782502	0.8931402	0.2029537	0.0000072	0.0000442	Lx6
Lx7	578.885557	1.0308086	0.2394896	0.0000098	0.0000595	Lx7
L1MdTf_III	704.552995	0.9075329	0.2125335	0.0000129	0.0000772	L1MdTf_III
L1MdFanc_I	399.020299	1.1827581	0.2836152	0.0000150	0.0000891	L1MdFanc_I
ORR1A4	67.010926	-1.3644583	0.3319866	0.0000154	0.0000902	ORR1A4
RSINE1	22.599000	-2.6051831	0.7351564	0.0000156	0.0000905	RSINE1
L1MdV_III	323.883563	0.7369276	0.1785021	0.0000276	0.0001580	L1MdV_III
MYSERV16_I-int	114.323833	1.7008265	0.4443093	0.0000292	0.0001650	MYSERV16_I-int
L1M2	127.275931	1.0455775	0.2592885	0.0000318	0.0001782	L1M2
Lx2A	20.831817	2.2633842	0.6499876	0.0000379	0.0002096	Lx2A
MTE2a-int	6.231468	4.0413221	1.5795004	0.0000432	0.0002365	MTE2a-int
MLT2B1	9.835016	-2.5096594	0.7683147	0.0000527	0.0002855	MLT2B1
MERVL_2A-int	407.117166	-1.4362885	0.3794716	0.0000540	0.0002891	MERVL_2A-int
RLTR4_Mm	76.552341	-1.2940614	0.3495774	0.0000921	0.0004881	RLTR4_Mm
L1MdN_I	122.046120	1.3771863	0.3763681	0.0000970	0.0005087	L1MdN_I
L1MA6	34.124975	1.4115555	0.3915022	0.0001137	0.0005896	L1MA6
Lx8	359.831636	0.9543648	0.2561592	0.0001232	0.0006327	Lx8
MTB-int	163.363455	-1.4618101	0.4184943	0.0001615	0.0008207	MTB-int
Lx2A1	30.744557	1.5644863	0.4671330	0.0002326	0.0011702	Lx2A1
MLT2B2	10.197537	3.3455515	1.4424663	0.0002351	0.0011707	MLT2B2
MTEa-int	36.291969	-1.5343385	0.4648835	0.0002909	0.0014344	MTEa-int
RLTR8	8.363612	-2.2118935	0.7717516	0.0003595	0.0017334	RLTR8
RodERV21-int	48.632387	-1.2858329	0.3847567	0.0003620	0.0017334	RodERV21-int
L1MdMus_II	249.154096	0.8340303	0.2402049	0.0003632	0.0017334	L1MdMus_II
L1MA4	36.721247	1.1700387	0.3462727	0.0003663	0.0017334	L1MA4
B1_Mur1	10.020472	-2.5766370	0.9763055	0.0003690	0.0017334	B1_Mur1
MTE2b	70.057237	-0.9525130	0.2799463	0.0004235	0.0019712	MTE2b
B1_Mur2	6.434517	-2.7449649	1.1218618	0.0004739	0.0021852	B1_Mur2
ORR1A3	26.352387	-1.5232512	0.4819495	0.0004825	0.0022044	ORR1A3
ORR1D2-int	23.826408	1.5902852	0.5111092	0.0005107	0.0023123	ORR1D2-int
L1Lx_III	357.830785	1.1649813	0.3550827	0.0005240	0.0023485	L1Lx_III
B1F	6.367802	-2.8180303	1.1956299	0.0005282	0.0023485	B1F
RLTR4_MM-int	291.627871	-1.1717526	0.3583481	0.0005404	0.0023818	RLTR4_MM-int
RLTR10E	7.493159	-2.1554952	0.7800456	0.0005511	0.0024074	RLTR10E
RLTR14	20.044601	-1.4129810	0.4601585	0.0007752	0.0033571	RLTR14
L1MdV_I	317.427103	0.7924764	0.2430386	0.0008080	0.0034526	L1MdV_I
MLTR25A	51.795100	-1.0983214	0.3456440	0.0008112	0.0034526	MLTR25A
RLTR20D	6.937101	-2.4028637	0.9746636	0.0008256	0.0034844	RLTR20D
Lx10	44.070532	1.1137268	0.3520439	0.0008367	0.0035013	Lx10
B1_Mur3	9.344677	-2.6122989	1.1357988	0.0008734	0.0036247	B1_Mur3
MT2A	98.008669	-0.8726402	0.2723910	0.0009244	0.0038047	MT2A
RLTR9D	19.182127	-1.4767071	0.4977173	0.0009887	0.0040358	RLTR9D
LTRIS_Mus	38.222974	-1.1510043	0.3726508	0.0010336	0.0041848	LTRIS_Mus
RMER19A	118.271952	-0.9172354	0.2914169	0.0010786	0.0043317	RMER19A
MT2B1	97.873435	-0.8569206	0.2718372	0.0011180	0.0044543	MT2B1
MIRb	11.325478	-1.7761208	0.6455480	0.0011649	0.0046043	MIRb
RLTR30	6.524432	2.3504260	0.9968690	0.0012105	0.0047468	RLTR30
ORR1B1	122.873112	-0.9612848	0.3114293	0.0012724	0.0049503	ORR1B1
RLTR10B2	9.027743	-1.7558937	0.6511021	0.0014219	0.0054893	RLTR10B2
L1Lx_IV	449.126064	0.8871662	0.2902007	0.0015030	0.0057577	L1Lx_IV
L1MD	21.876789	1.3641639	0.4882037	0.0020144	0.0076576	L1MD
IAPLTR2b	10.243263	-1.5003304	0.5595692	0.0023010	0.0086809	IAPLTR2b
LTRIS_Mm	31.286228	-1.4540833	0.5391561	0.0023615	0.0088424	LTRIS_Mm
L1M3	21.885271	1.0933917	0.3918126	0.0028775	0.0106939	L1M3
RLTR10F	8.012838	-1.7378771	0.7193622	0.0032329	0.0118459	RLTR10F
L1MC1	38.817103	1.0797385	0.3918161	0.0032497	0.0118459	L1MC1
ORR1C1-int	111.147533	-0.9173916	0.3268769	0.0032728	0.0118459	ORR1C1-int
ORR1D1-int	29.967482	1.0638805	0.3857300	0.0032826	0.0118459	ORR1D1-int
RMER17D2	16.936350	1.6289518	0.6574210	0.0033116	0.0118645	RMER17D2
RLTR26	5.657786	-1.7239898	0.7313962	0.0038667	0.0137546	RLTR26
RLTR6B_Mm	27.211544	1.2579207	0.4827194	0.0040818	0.0144165	RLTR6B_Mm
L1MD3	6.116518	2.2366977	1.1729098	0.0041754	0.0146434	L1MD3
Lx4A	329.849988	0.8692736	0.3182566	0.0042982	0.0149687	Lx4A
RLTR31B2	15.518438	-1.3578199	0.5365478	0.0044015	0.0152219	RLTR31B2
RLTR40	239.861664	1.2074106	0.4700727	0.0048496	0.0166559	RLTR40
MTE2b-int	14.996555	1.7707989	0.8016756	0.0051579	0.0175934	MTE2b-int
MTB_Mm	34.776925	-1.1247978	0.4434630	0.0058744	0.0198937	MTB_Mm
L1MA9	15.660769	1.4685709	0.6223473	0.0059122	0.0198937	L1MA9
L1MA5	15.661575	1.2376916	0.5028369	0.0062925	0.0209654	L1MA5
MLT2B3	7.710680	-1.5536229	0.6813282	0.0063149	0.0209654	MLT2B3
RLTR31M	8.534716	-1.8967689	0.9410811	0.0063826	0.0210500	RLTR31M
L2b	7.051410	-1.6782019	0.7704885	0.0065549	0.0214759	L2b
SRV_MM-int	20.273623	-1.5725603	0.7027208	0.0068020	0.0221397	SRV_MM-int
RLTR22_Mur	25.690892	1.1669864	0.4744921	0.0069202	0.0223784	RLTR22_Mur
RLTR50B	18.024782	-1.4661935	0.6392412	0.0070370	0.0226091	RLTR50B
RLTR13A	25.414757	1.3294868	0.5698430	0.0078164	0.0249522	RLTR13A
ERVB7_2B-LTR_MM	9.142095	-1.6268388	0.7608989	0.0078866	0.0250139	ERVB7_2B-LTR_MM
RLTR1B	20.481928	-1.1532649	0.4777133	0.0079613	0.0250139	RLTR1B
RLTR1B-int	1591.826450	-1.2813355	0.5451702	0.0079943	0.0250139	RLTR1B-int
RMER15	120.195830	-0.9085463	0.3627039	0.0080366	0.0250139	RMER15
RLTR5_Mm	8.116408	1.8455988	0.9477917	0.0081185	0.0251119	RLTR5_Mm
Lx4B	126.605343	0.9453011	0.3834193	0.0086688	0.0266484	Lx4B
LTRIS4A	12.567590	-1.3303933	0.5875210	0.0093096	0.0284427	LTRIS4A
L1MB5	152.030760	1.0483274	0.4417822	0.0100348	0.0304715	L1MB5
RMER13B	45.411250	1.1013151	0.4700650	0.0102404	0.0309075	RMER13B
RLTR17D_Mm	21.104047	1.2604291	0.5613206	0.0107734	0.0323202	RLTR17D_Mm
RMER17C-int	36.488428	-1.0011011	0.4259366	0.0112053	0.0334147	RMER17C-int
RLTR44-int	14.240961	1.2298800	0.5489024	0.0113637	0.0336852	RLTR44-int
L1ME3	4.256882	1.9926367	1.2681613	0.0116181	0.0342355	L1ME3
RLTR21	90.609347	1.0113934	0.4355527	0.0119449	0.0349916	RLTR21
RMER19B2	81.220106	-0.7764506	0.3300350	0.0136400	0.0397206	RMER19B2
MLT1F2	11.118506	-1.4204712	0.6939891	0.0137205	0.0397206	MLT1F2
B4	60.496285	-0.7334772	0.3107468	0.0137985	0.0397206	B4
RMER16A2	4.202485	-1.7713149	1.0178491	0.0139269	0.0398598	RMER16A2
RLTR9A3	5.228491	-1.5789157	0.8259947	0.0141756	0.0403397	RLTR9A3
L1MD1	8.954970	1.3562127	0.6574749	0.0146033	0.0413208	L1MD1
ORR1D-int	6.911431	1.5542109	0.8260811	0.0157468	0.0443045	ORR1D-int
RLTR13D2	5.374658	1.6714534	0.9519665	0.0163208	0.0456615	RLTR13D2
MMERVK10D3_I-int	83.817944	-1.2613345	0.6173789	0.0175414	0.0488024	MMERVK10D3_I-int
MuLV-int	88.085682	-0.8177790	0.3650919	0.0177296	0.0490519	MuLV-int
IAPEY4_LTR	3.125807	-1.7432218	1.0859538	0.0183909	0.0506004	IAPEY4_LTR
ERVL-B4-int	55.858512	-0.9637916	0.4453742	0.0187826	0.0513941	ERVL-B4-int
MLT1F	6.017937	-1.3496072	0.6923588	0.0190351	0.0518006	MLT1F
ORR1B2	31.177512	-0.7773515	0.3524724	0.0200032	0.0541390	ORR1B2
RLTR42-int	15.418864	-1.0766467	0.5174762	0.0203549	0.0547932	RLTR42-int
RMER13A2	12.492508	1.1251630	0.5537356	0.0215332	0.0576533	RMER13A2
RMER20B	19.255719	1.0839094	0.5359830	0.0231467	0.0616421	RMER20B
RMER17A2	19.506885	0.8767849	0.4157017	0.0233641	0.0618597	RMER17A2
RMER10A	28.334374	-0.8037703	0.3770610	0.0235516	0.0618597	RMER10A
MTE-int	57.013055	0.8140856	0.3826750	0.0236011	0.0618597	MTE-int
L1M5	29.049602	0.9089368	0.4349558	0.0237712	0.0619794	L1M5
L1M4b	10.697815	1.4270163	0.8026246	0.0240171	0.0622944	L1M4b
LTR16C	23.156056	-1.3984707	0.7829780	0.0247631	0.0638966	LTR16C
RMER16-int	669.692891	0.8829428	0.4277081	0.0258889	0.0664413	RMER16-int
ERVB4_1B-I_MM	86.497439	-0.6647163	0.3116040	0.0260162	0.0664413	ERVB4_1B-I_MM
MTB	56.236930	-0.7519511	0.3577590	0.0264042	0.0667896	MTB
RLTR20B5_MM	9.118252	1.3585610	0.7611278	0.0264535	0.0667896	RLTR20B5_MM
L1MD2	9.894983	1.1437988	0.5928901	0.0265549	0.0667896	L1MD2
RLTR16B_MM	13.310764	1.2590413	0.6806525	0.0269350	0.0673294	RLTR16B_MM
IAPEY2_LTR	9.759280	-1.2833835	0.7009997	0.0270399	0.0673294	IAPEY2_LTR
RLTR1A2_MM	12.240512	-1.1450241	0.6181695	0.0313290	0.0776212	RLTR1A2_MM
MLT1K	15.846868	-1.0606028	0.5641642	0.0327755	0.0808031	MLT1K
IAPEY_LTR	9.261945	-1.0903987	0.5868352	0.0331519	0.0813282	IAPEY_LTR
RLTR13G	50.979141	-0.8901286	0.4591192	0.0344712	0.0841503	RLTR13G
RMER10B	9.158120	-1.1371549	0.6324553	0.0354730	0.0861733	RMER10B
RLTR16	13.075378	-1.0959973	0.6035736	0.0360173	0.0870710	RLTR16
L1MdTf_II	1552.234049	-0.6497538	0.3278687	0.0378477	0.0910538	L1MdTf_II
L1MCa	20.478549	0.8609278	0.4543924	0.0391254	0.0936752	L1MCa
RLTR13D3	8.631173	1.2040353	0.7095998	0.0396548	0.0944684	RLTR13D3
L2	33.259231	0.8395448	0.4429628	0.0398361	0.0944684	L2
ERVB7_2-LTR_MM	5.257771	-1.2903663	0.8063271	0.0416622	0.0983307	ERVB7_2-LTR_MM
L1MEc	15.544808	0.8835010	0.4771574	0.0421355	0.0988046	L1MEc
MLT1G3	4.087163	-1.2847315	0.8043385	0.0422598	0.0988046	MLT1G3
RLTR11A	35.907051	-0.7269929	0.3810799	0.0424977	0.0988965	RLTR11A

E4.0 ICM vs 8c
	baseMean	log2FoldChange	lfcSE	pvalue	padj	repName
ORR1C1-int	111.147533	2.5243243	0.3348230	0.0000000	0.0000000	ORR1C1-int
MT-int	1264.500140	3.3709456	0.6286647	0.0000000	0.0000000	MT-int
RMER16-int	669.692891	2.4993574	0.4292497	0.0000000	0.0000000	RMER16-int
L1MdA_VI	253.849184	-1.7593707	0.2827070	0.0000000	0.0000000	L1MdA_VI
ORR1A0	232.436518	1.8796426	0.3484224	0.0000000	0.0000002	ORR1A0
ETnERV-int	552.777898	1.8944972	0.3550816	0.0000000	0.0000002	ETnERV-int
Lx5b	172.899740	-1.4645226	0.2911929	0.0000001	0.0000049	Lx5b
Lx3_Mus	216.577970	-1.2344396	0.2502111	0.0000002	0.0000133	Lx3_Mus
MMETn-int	4901.889603	1.6679805	0.3595178	0.0000002	0.0000138	MMETn-int
MLT1K	15.846868	2.2990192	0.5746744	0.0000003	0.0000168	MLT1K
MTEb	31.164984	1.6973506	0.3834251	0.0000005	0.0000276	MTEb
RLTR14-int	43.697224	1.4978224	0.3329870	0.0000008	0.0000360	RLTR14-int
L1MdA_VII	258.785943	-1.3909388	0.3136604	0.0000014	0.0000593	L1MdA_VII
Lx9	334.311664	-0.9032250	0.1938445	0.0000015	0.0000593	Lx9
RLTR1B-int	1591.826450	1.9503996	0.5260407	0.0000041	0.0001539	RLTR1B-int
ERVB4_2-I_MM	776.196549	-1.6955598	0.4382729	0.0000059	0.0002110	ERVB4_2-I_MM
Lx2B	125.060571	-1.4675093	0.3669323	0.0000076	0.0002442	Lx2B
L1MdA_III	614.797032	-0.8657554	0.2005018	0.0000077	0.0002442	L1MdA_III
L1MdF_I	337.797214	-0.9157118	0.2147169	0.0000091	0.0002706	L1MdF_I
L1M2	127.275931	-1.1828185	0.2885013	0.0000109	0.0003088	L1M2
LTRIS2	298.700826	1.7669930	0.4913191	0.0000129	0.0003486	LTRIS2
MMERGLN-int	490.479182	1.1981564	0.2985792	0.0000152	0.0003921	MMERGLN-int
L1MdF_IV	434.190199	-1.5041661	0.3974884	0.0000162	0.0003969	L1MdF_IV
MYSERV6-int	168.412775	1.0045362	0.2457502	0.0000168	0.0003969	MYSERV6-int
L1MdF_II	171.072017	-1.0989065	0.2729269	0.0000180	0.0004086	L1MdF_II
Lx3A	152.629809	-1.6259333	0.4549788	0.0000238	0.0005206	Lx3A
B3	175.338095	1.3195356	0.3462854	0.0000255	0.0005364	B3
RLTR30E_MM	28.654635	1.6371939	0.4700242	0.0000318	0.0006377	RLTR30E_MM
L1MdMus_I	180.467799	-1.0304975	0.2629821	0.0000326	0.0006377	L1MdMus_I
Lx7	578.885557	-0.9369167	0.2378815	0.0000357	0.0006763	Lx7
BGLII_A	8.059379	1.9537154	0.6500441	0.0000404	0.0007394	BGLII_A
L1MdTf_I	1497.502375	1.1380423	0.3003760	0.0000439	0.0007793	L1MdTf_I
L1_Mur2	295.244079	-0.8471880	0.2173662	0.0000492	0.0008473	L1_Mur2
MuRRS4-int	100.894595	1.4541412	0.4136276	0.0000529	0.0008787	MuRRS4-int
L1MdTf_II	1552.234049	1.1777388	0.3176317	0.0000551	0.0008787	L1MdTf_II
L1MdGf_II	250.695268	-0.8096022	0.2090330	0.0000577	0.0008787	L1MdGf_II
B2_Mm2	544.932679	1.5349260	0.4493896	0.0000580	0.0008787	B2_Mm2
RMER15	120.195830	1.2701752	0.3498102	0.0000588	0.0008787	RMER15
Lx8b	170.082455	-0.9205339	0.2464117	0.0000839	0.0012213	Lx8b
B3A	58.354256	1.3207693	0.3875504	0.0001168	0.0016420	B3A
LTRIS4A	12.567590	1.5915396	0.5064831	0.0001185	0.0016420	LTRIS4A
RLTR13D6	64.828745	1.4892677	0.4621865	0.0001312	0.0017438	RLTR13D6
B2_Mm1t	1112.751367	1.5554082	0.4938303	0.0001320	0.0017438	B2_Mm1t
MTA_Mm	4718.690175	1.1571305	0.3346592	0.0001494	0.0019284	MTA_Mm
ETnERV2-int	242.978125	1.0819550	0.3116270	0.0001681	0.0021216	ETnERV2-int
Lx3C	91.180293	-0.9773177	0.2779765	0.0001766	0.0021808	Lx3C
L1_Mur1	114.598750	-0.9397128	0.2667726	0.0001847	0.0022317	L1_Mur1
Lx2	359.521136	-1.0145190	0.2927376	0.0001980	0.0023429	Lx2
B2_Mm1a	1713.375648	1.5253076	0.5017384	0.0002072	0.0024017	B2_Mm1a
ORR1A0-int	3477.346922	1.2945640	0.3990076	0.0002225	0.0025276	ORR1A0-int
IAPEY3-int	83.711688	-1.2929657	0.4006082	0.0002367	0.0026367	IAPEY3-int
RLTR45-int	6971.091058	-1.2159824	0.3714628	0.0002489	0.0027183	RLTR45-int
MMERVK9E_I-int	155.179063	1.1592905	0.3541742	0.0002870	0.0030752	MMERVK9E_I-int
L1MdF_V	444.474972	-1.0976083	0.3361104	0.0003402	0.0035782	L1MdF_V
ERVB7_1-LTR_MM	32.784875	1.2856410	0.4161325	0.0003817	0.0039422	ERVB7_1-LTR_MM
L1Lx_I	389.248277	-0.5445988	0.1607634	0.0005273	0.0052588	L1Lx_I
L1MdFanc_II	334.287560	-0.7600937	0.2292843	0.0005277	0.0052588	L1MdFanc_II
RLTR13G	50.979141	1.2547097	0.4174125	0.0005438	0.0053253	RLTR13G
L1MdGf_I	625.823714	0.8709507	0.2708819	0.0006313	0.0060778	L1MdGf_I
LTRIS_Mm	31.286228	1.3558746	0.4885164	0.0008013	0.0074824	LTRIS_Mm
B1_Mm	56.581553	1.5441723	0.6159797	0.0008036	0.0074824	B1_Mm
MTA_Mm-int	52698.165407	1.3987787	0.5150988	0.0008211	0.0075223	MTA_Mm-int
L1MdA_V	111.829895	0.8363784	0.2695664	0.0009811	0.0087830	L1MdA_V
Lx3B	79.236226	-0.9940435	0.3298583	0.0009896	0.0087830	Lx3B
IAPLTR3-int	39.910505	-1.3883296	0.5234998	0.0010081	0.0088094	IAPLTR3-int
L1MdA_II	620.303707	-0.7717069	0.2529253	0.0012874	0.0110793	L1MdA_II
MER34B-int	25.201147	1.4191707	0.5668053	0.0013106	0.0111110	MER34B-int
MuLV-int	88.085682	1.0663938	0.3722768	0.0013569	0.0113337	MuLV-int
RLTR6-int	255.580418	-0.9078275	0.3069571	0.0013982	0.0114486	RLTR6-int
L1Lx_II	112.641418	-0.9580594	0.3281899	0.0014372	0.0114486	L1Lx_II
L1MB7	56.370275	-1.3656944	0.5386521	0.0014672	0.0114486	L1MB7
ORR1B1-int	140.071728	0.8760489	0.2959727	0.0014677	0.0114486	ORR1B1-int
ORR1A2	142.223361	0.8256466	0.2769155	0.0014883	0.0114486	ORR1A2
L1_Rod	96.130374	-0.8743906	0.2958247	0.0014915	0.0114486	L1_Rod
Lx5	315.182188	-0.6081086	0.1991234	0.0015776	0.0119475	Lx5
RLTRETN_Mm	28.042346	1.0705559	0.3891753	0.0018915	0.0141367	RLTRETN_Mm
Lx2A1	30.744557	-1.2659555	0.4987061	0.0020150	0.0148640	Lx2A1
RLTR41	19.416434	1.2082189	0.4739344	0.0023266	0.0169424	RLTR41
RLTR4_Mm	76.552341	0.9469464	0.3451830	0.0025189	0.0181105	RLTR4_Mm
RLTR10F	8.012838	1.3962189	0.6349027	0.0027157	0.0192813	RLTR10F
RLTR13A3	22.969320	1.2169241	0.4947494	0.0028554	0.0200228	RLTR13A3
ORR1A4-int	278.120957	0.9521745	0.3563160	0.0030721	0.0212797	ORR1A4-int
MMERGLN_LTR	22.589795	0.9912608	0.3763388	0.0031645	0.0216556	MMERGLN_LTR
MURVY-int	55.737237	1.3013008	0.5734544	0.0033807	0.0228599	MURVY-int
B1_Mus1	68.244099	1.3264883	0.6320112	0.0042721	0.0280858	B1_Mus1
ORR1C1	37.569853	1.0004221	0.3975306	0.0043005	0.0280858	ORR1C1
RLTR8	8.363612	1.3580152	0.6751252	0.0043019	0.0280858	RLTR8
MLT2B3	7.710680	-1.3153642	0.9188799	0.0050388	0.0325234	MLT2B3
L1MdA_IV	171.565137	-0.6160097	0.2352814	0.0060943	0.0388936	L1MdA_IV
ORR1A4	67.010926	0.8583103	0.3503192	0.0068439	0.0431926	ORR1A4
RLTR45	153.507229	-1.0197335	0.4420152	0.0070812	0.0441992	RLTR45
RLTR20B1	21.581115	1.1331124	0.5234038	0.0072815	0.0449551	RLTR20B1
MLT1F2-int	2.442432	1.1063510	0.9985434	0.0076913	0.0469751	MLT1F2-int
RLTR30D_MM	3.452143	1.2901683	0.7564702	0.0078662	0.0475317	RLTR30D_MM
MT2_Mm	2751.765261	0.8683823	0.3658448	0.0082339	0.0492303	MT2_Mm
RLTR10-int	690.924548	-0.7810434	0.3279625	0.0093848	0.0555266	RLTR10-int
RLTR44-int	14.240961	-1.2240400	0.7030466	0.0105382	0.0617082	RLTR44-int
B1_Mur1	10.020472	1.2234380	0.8323263	0.0108757	0.0630350	B1_Mur1
MER21C	18.853208	0.9907587	0.4641261	0.0114093	0.0654594	MER21C
RLTR4_MM-int	291.627871	0.7777264	0.3419046	0.0124592	0.0704907	RLTR4_MM-int
MTC-int	215.893874	0.7715455	0.3392745	0.0126040	0.0704907	MTC-int
RLTR9D	19.182127	0.9627047	0.4544912	0.0126585	0.0704907	RLTR9D
MYSERV16_I-int	114.323833	0.8404347	0.3786997	0.0128379	0.0707954	MYSERV16_I-int
RLTR9E	55.788276	0.8735940	0.4002990	0.0131856	0.0717209	RLTR9E
RLTR19-int	81.402293	0.8756034	0.4019589	0.0132608	0.0717209	RLTR19-int
RLTR40	239.861664	0.9247670	0.4339312	0.0133845	0.0717209	RLTR40
LTRIS_Mus	38.222974	0.7989686	0.3645811	0.0148036	0.0779155	LTRIS_Mus
B1_Mur2	6.434517	1.1198876	0.8988477	0.0149104	0.0779155	B1_Mur2
L1M5	29.049602	-0.9594229	0.4687479	0.0149521	0.0779155	L1M5
MMERVK9C_I-int	274.204475	0.7041211	0.3164536	0.0158318	0.0817499	MMERVK9C_I-int
RLTR30D2_MM	10.882992	-1.1349189	0.7974234	0.0180351	0.0922875	RLTR30D2_MM
L1MCc	3.212565	1.1107648	0.8523783	0.0184397	0.0935156	L1MCc
RLTR20B2	4.172151	-1.0511086	0.9118549	0.0196443	0.0987431	RLTR20B2

3.1 MA-plots

In the MA-plots:

The threshold used for a dot to be coloured based on repFamily is p-value adjusted < 0.1.
Transposable elements whose mean expression > 10 and log2FoldChange > 0.2 (or < -0.2) are labeled (but labeling is limited by max.overlap parameter).

3.2 Overlap between morula-to-blastocysts’ DESeq results

The ICM and E3.5 ICM libraries can be used almost interchangeably, while a significant fraction of DE TEs are specific of ICM or trophectoderm, thus it will be good to combine trophectoderm and ICM DESeq results for comparison with TEs diff. expr. in OgtT931del mutant blastocysts, which are whole embryo samples.

sessionInfo()

## R version 4.1.3 (2022-03-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.6 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] RColorBrewer_1.1-3          ggpubr_0.5.0               
##  [3] ggrepel_0.9.2               gridExtra_2.3              
##  [5] DESeq2_1.34.0               SummarizedExperiment_1.24.0
##  [7] Biobase_2.54.0              MatrixGenerics_1.6.0       
##  [9] matrixStats_0.62.0          GenomicRanges_1.46.1       
## [11] GenomeInfoDb_1.30.1         IRanges_2.28.0             
## [13] S4Vectors_0.32.4            BiocGenerics_0.40.0        
## [15] pheatmap_1.0.12             data.table_1.14.6          
## [17] ggplot2_3.4.0              
## 
## loaded via a namespace (and not attached):
##  [1] bitops_1.0-7           bit64_4.0.5            httr_1.4.4            
##  [4] tools_4.1.3            backports_1.4.1        bslib_0.4.1           
##  [7] irlba_2.3.5.1          utf8_1.2.2             R6_2.5.1              
## [10] DBI_1.1.3              colorspace_2.0-3       withr_2.5.0           
## [13] tidyselect_1.2.0       bit_4.0.5              compiler_4.1.3        
## [16] cli_3.4.1              DelayedArray_0.20.0    labeling_0.4.2        
## [19] sass_0.4.2             scales_1.2.1           SQUAREM_2021.1        
## [22] genefilter_1.76.0      mixsqp_0.3-48          stringr_1.4.1         
## [25] digest_0.6.30          rmarkdown_2.18         XVector_0.34.0        
## [28] pkgconfig_2.0.3        htmltools_0.5.3        invgamma_1.1          
## [31] highr_0.9              fastmap_1.1.0          rlang_1.0.6           
## [34] rstudioapi_0.14        RSQLite_2.2.18         prettydoc_0.4.1       
## [37] farver_2.1.1           jquerylib_0.1.4        generics_0.1.3        
## [40] jsonlite_1.8.3         BiocParallel_1.28.3    car_3.1-1             
## [43] dplyr_1.0.10           RCurl_1.98-1.9         magrittr_2.0.3        
## [46] GenomeInfoDbData_1.2.7 Matrix_1.5-3           Rcpp_1.0.9            
## [49] munsell_0.5.0          fansi_1.0.3            abind_1.4-5           
## [52] lifecycle_1.0.3        stringi_1.7.8          yaml_2.3.6            
## [55] carData_3.0-5          zlibbioc_1.40.0        grid_4.1.3            
## [58] blob_1.2.3             parallel_4.1.3         crayon_1.5.2          
## [61] lattice_0.20-45        Biostrings_2.62.0      splines_4.1.3         
## [64] annotate_1.72.0        KEGGREST_1.34.0        locfit_1.5-9.6        
## [67] knitr_1.40             pillar_1.8.1           ggsignif_0.6.4        
## [70] codetools_0.2-18       geneplotter_1.72.0     XML_3.99-0.12         
## [73] glue_1.6.2             evaluate_0.18          png_0.1-7             
## [76] vctrs_0.5.1            gtable_0.3.1           purrr_0.3.5           
## [79] tidyr_1.2.1            assertthat_0.2.1       ashr_2.2-54           
## [82] cachem_1.0.6           xfun_0.35              xtable_1.8-4          
## [85] broom_1.0.1            rstatix_0.7.1          survival_3.2-13       
## [88] truncnorm_1.0-8        tibble_3.1.8           AnnotationDbi_1.56.2  
## [91] memoise_2.0.1

Transposable elements (TE) analysis in public datasets spanning preimplantation mouse development

Sara Formichetti

April 11th, 2023