GEO series
Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in mouse early embryos [ATAC-seq]
GSE264614
Mus musculus
Genome binding/occupancy profiling by high throughput sequencing
44 samples
Submitted 2024/10/14
Platform GPL19057
Summary
During the first lineage segregation, mammalian embryos generate the inner cell mass (ICM) and trophectoderm (TE). ICM gives rise to the epiblast (EPI) that forms all cell types of the body, an ability referred to as pluripotency. The molecular mechanisms that induce pluripotency in embryos remain incompletely elucidated. Using knockout (KO) mouse models in conjunction with low-input ATAC-seq and RNA-seq, we found that Oct4 and Sox2 gradually come into play in the early ICM, coinciding with the initiation of Sox2 expression. Oct4 and Sox2 directly activate the pluripotency-related genes through the corresponding OCT-SOX enhancers in the early ICM. Furthermore, we observed a substantial reorganization of chromatin landscape and transcriptome from the morula to the early ICM stages, which was partially driven by Oct4 and Sox2, highlighting their pivotal role in promoting the developmental trajectory towards the ICM. Our study provides new insights into the establishment of the pluripotency network in mouse preimplantation embryos.
Published in
Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in early mouse embryos
Hou Y, Nie Z, Jiang Q et al.
· eLife 2025
· PMID 40014376
· doi:10.7554/eLife.100735
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE264614_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 44 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA991530 and SRA study SRP447418. Searching any of these in the dataset finder brings you back here.
Study design
12 conditions, mostly with about 4 replicates each
ATAC-seq_Oct4_Ctrl_EarlyICM ×4
ATAC-seq_Oct4_KO_EarlyICM ×4
ATAC-seq_Oct4_Ctrl_LateICM ×4
ATAC-seq_Oct4_KO_LateICM ×4
ATAC-seq_Sox2_Ctrl_EarlyICM ×4
ATAC-seq_Sox2_KO_EarlyICM ×4
ATAC-seq_Oct4_Ctrl_Morula ×3
ATAC-seq_Oct4_KO_Morula ×3
+4 more
Supports a between-group comparison across 40 samples.
12 replicated groups read from the first 40 of 44 sample titles; they account for 40 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM8223911 ATAC-seq_Oct4_Ctrl_Morula_1
- GSM8223912 ATAC-seq_Oct4_KO_Morula_1
- GSM8223913 ATAC-seq_Oct4_Ctrl_Morula_2
- GSM8223914 ATAC-seq_Oct4_KO_Morula_2
- GSM8223915 ATAC-seq_Oct4_Ctrl_Morula_3
- GSM8223916 ATAC-seq_Oct4_KO_Morula_3
- GSM8223917 ATAC-seq_Oct4_Ctrl_LateMorula_1
- GSM8223918 ATAC-seq_Oct4_KO_LateMorula_1
- GSM8223919 ATAC-seq_Oct4_Ctrl_LateMorula_2
- GSM8223920 ATAC-seq_Oct4_KO_LateMorula_2
- GSM8223921 ATAC-seq_Oct4_Ctrl_LateMorula_3
- GSM8223922 ATAC-seq_Oct4_KO_LateMorula_3
- GSM8223923 ATAC-seq_Oct4_Ctrl_EarlyICM_1
- GSM8223924 ATAC-seq_Oct4_KO_EarlyICM_1
- GSM8223925 ATAC-seq_Oct4_Ctrl_EarlyICM_2
- GSM8223926 ATAC-seq_Oct4_KO_EarlyICM_2
- GSM8223927 ATAC-seq_Oct4_Ctrl_EarlyICM_3
- GSM8223928 ATAC-seq_Oct4_KO_EarlyICM_3
- GSM8223929 ATAC-seq_Oct4_Ctrl_EarlyICM_4
- GSM8223930 ATAC-seq_Oct4_KO_EarlyICM_4
- GSM8223931 ATAC-seq_Oct4_Ctrl_LateICM_1
- GSM8223932 ATAC-seq_Oct4_KO_LateICM_1
- GSM8223933 ATAC-seq_Oct4_Ctrl_LateICM_2
- GSM8223934 ATAC-seq_Oct4_KO_LateICM_2
- GSM8223935 ATAC-seq_Oct4_Ctrl_LateICM_3
- GSM8223936 ATAC-seq_Oct4_KO_LateICM_3
- GSM8223937 ATAC-seq_Oct4_Ctrl_LateICM_4
- GSM8223938 ATAC-seq_Oct4_KO_LateICM_4
- GSM8223939 ATAC-seq_Sox2_Ctrl_EarlyICM_1
- GSM8223940 ATAC-seq_Sox2_KO_EarlyICM_1
- GSM8223941 ATAC-seq_Sox2_Ctrl_EarlyICM_2
- GSM8223942 ATAC-seq_Sox2_KO_EarlyICM_2
- GSM8223943 ATAC-seq_Sox2_Ctrl_EarlyICM_3
- GSM8223944 ATAC-seq_Sox2_KO_EarlyICM_3
- GSM8223945 ATAC-seq_Sox2_Ctrl_EarlyICM_4
- GSM8223946 ATAC-seq_Sox2_KO_EarlyICM_4
- GSM8223947 ATAC-seq_Sox2_Ctrl_LateICM_1
- GSM8223948 ATAC-seq_Sox2_KO_LateICM_1
- GSM8223949 ATAC-seq_Sox2_Ctrl_LateICM_2
- GSM8223950 ATAC-seq_Sox2_KO_LateICM_2
+ 4 more — browse all 44 samples with per-sample file links →
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