Cohesin-mediated loop extrusion and enhancer-associated factors additively contribute to Sox2 looping with its distal enhancer.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 81 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 81 samples: 33 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Cohesin-mediated loop extrusion and enhancer-associated factors additively contribute to Sox2 looping with its distal enhancerGenes & development · 2026
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE306301_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1310430 and SRA study SRP612379. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 72 samples.
How we read this: 33 replicated groups read from 81 sample titles; they account for 72 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM9196963 DP_ATAC-seq_rep1 DP_ATAC-seq
- GSM9196964 DP_ATAC-seq_rep2 DP_ATAC-seq
- GSM9196965 GFP_ATAC-seq_rep1 GFP_ATAC-seq
- GSM9196966 GFP_ATAC-seq_rep2 GFP_ATAC-seq
- GSM9196967 RFP_ATAC-seq_rep1 RFP_ATAC-seq
- GSM9196968 RFP_ATAC-seq_rep2 RFP_ATAC-seq
- GSM9196969 Ctcf_0H_4C-seq_rep1 Ctcf_0H_4C-seq
- GSM9196970 Ctcf_0H_4C-seq_rep2 Ctcf_0H_4C-seq
- GSM9196971 Ctcf_3H_4C-seq_rep1 Ctcf_3H_4C-seq
- GSM9196972 Ctcf_3H_4C-seq_rep2 Ctcf_3H_4C-seq
- GSM9196973 Ctcf_6H_4C-seq_rep1 Ctcf_6H_4C-seq
- GSM9196974 Ctcf_6H_4C-seq_rep2 Ctcf_6H_4C-seq
- GSM9196975 DMSO_6h_DMSO_3h_4C-seq_rep1 DMSO_6h_DMSO_3h_4C-seq
- GSM9196976 DMSO_6h_DMSO_3h_4C-seq_rep2 DMSO_6h_DMSO_3h_4C-seq
- GSM9196977 DMSO_6h_dTAG_3h_4C-seq_rep1 DMSO_6h_dTAG_3h_4C-seq
- GSM9196978 DMSO_6h_dTAG_3h_4C-seq_rep2 DMSO_6h_dTAG_3h_4C-seq
- GSM9196979 DP_both_VP
- GSM9196980 DP_DMSO_3h_4C-seq_rep1 DP_DMSO_3h_4C-seq
- GSM9196981 DP_DMSO_3h_4C-seq_rep2 DP_DMSO_3h_4C-seq
- GSM9196982 DP_DMSO_3h_4C-seq_rep3 DP_DMSO_3h_4C-seq
- GSM9196983 DP_dTAG_3h_4C-seq_rep1 DP_dTAG_3h_4C-seq
- GSM9196984 DP_dTAG_3h_4C-seq_rep2 DP_dTAG_3h_4C-seq
- GSM9196985 DP_dTAG_3h_4C-seq_rep3 DP_dTAG_3h_4C-seq
- GSM9196986 DP_prom_only
- GSM9196987 DP_SCR_only_4C-seq_rep1 DP_SCR_only_4C-seq
- GSM9196988 DP_SCR_only_4C-seq_rep2 DP_SCR_only_4C-seq
- GSM9196989 GFP_both_VP
- GSM9196990 GFP_DMSO_3h_4C-seq_rep1 GFP_DMSO_3h_4C-seq
- GSM9196991 GFP_DMSO_3h_4C-seq_rep2 GFP_DMSO_3h_4C-seq
- GSM9196992 GFP_DMSO_3h_4C-seq_rep3 GFP_DMSO_3h_4C-seq
- GSM9196993 GFP_dTAG_3h_4C-seq_rep1 GFP_dTAG_3h_4C-seq
- GSM9196994 GFP_dTAG_3h_4C-seq_rep2 GFP_dTAG_3h_4C-seq
- GSM9196995 GFP_dTAG_3h_4C-seq_rep3 GFP_dTAG_3h_4C-seq
- GSM9196996 GFP_prom_only
- GSM9196997 GFP_SCR_only_4C-seq_rep1 GFP_SCR_only_4C-seq
- GSM9196998 GFP_SCR_only_4C-seq_rep2 GFP_SCR_only_4C-seq
- GSM9196999 iBet_18h_DMSO_3h_4C-seq_rep1 iBet_18h_DMSO_3h_4C-seq
- GSM9197000 iBet_18h_DMSO_3h_4C-seq_rep2 iBet_18h_DMSO_3h_4C-seq
- GSM9197001 iBet_18h_dTAG_3h_4C-seq_rep1 iBet_18h_dTAG_3h_4C-seq
- GSM9197002 iBet_18h_dTAG_3h_4C-seq_rep2 iBet_18h_dTAG_3h_4C-seq
+ 41 more — browse all 81 samples with per-sample file links →
- GSE306297 Cohesin-mediated loop extrusion and enhancer-associated factors additively contribute to Sox2 looping with its distal enhancer [ATAC-seq] 6 samples shares sox2, enhancer-associated, cohesin-mediated, additively, contribute, extrusion, enhancer, factors
- GSE90895 Cooperative binding of Oct4, Sox2, and Klf4 with stage-specific transcription factors orchestrates reprogramming 150 samples shares sox2, factors
- GSE90893 Cooperative binding of Oct4, Sox2, and Klf4 with stage-specific transcription factors orchestrates reprogramming [ChIP-seq] 119 samples shares sox2, factors
- GSE240327 A set of Sox2-dependent OSN enhancers mediates the immediate response to neural induction and default neural differentiation of embryonic stem cells 40 samples shares sox2, enhancer
- GSE90894 Cooperative binding of Oct4, Sox2, and Klf4 with stage-specific transcription factors orchestrates reprogramming [RNA-seq] 22 samples shares sox2, factors
- GSE263925 Genome-wide identification of target genes for the transcription factors Sox2 and Sox3 in differentiated primary mouse oligodendrocytes 4 samples shares sox2, factors
- GSE222746 Enhanced activities of OCT4 and SOX2 facilitates epigenetic reprogramming by modulating cell cycle 460 samples shares sox2
- GSE222745 Enhanced activities of OCT4 and SOX2 facilitates epigenetic reprogramming by modulating cell cycle [scRNA-Seq] 422 samples shares sox2
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.