Promoter- and Enhancer-Dependent Cohesin Loading Initiates Chromosome Looping to Fold Tcrb Loci for Long-Range Recombination
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: 20 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
- Promoter- and enhancer-dependent cohesin loading initiates chromosome looping to fold Tcrb loci for long-range recombinationCell reports · 2025
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 GSE296315_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 PRJNA1258885 and SRA study SRP583065. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 42 samples.
How we read this: 20 replicated groups read from 81 sample titles; they account for 42 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.
- GSM8968329 WT DNs ChIP H3K4me3 1 WT DNs ChIP H3K4me3
- GSM8968330 V1P KO/KO DNs ChIP H3K4me3 1
- GSM8968331 V1P KO/KO DNs input
- GSM8968332 WT DNs ChIP H3K4me3 2 WT DNs ChIP H3K4me3
- GSM8968333 WT DNs input
- GSM8968334 V1 TxS DNs ChIP H3K4me3 1 V1 TxS DNs ChIP H3K4me3
- GSM8968335 V1 TxS DNs input
- GSM8968336 V1 TxS DNs ChIP H3K4me3 2 V1 TxS DNs ChIP H3K4me3
- GSM8968340 R1KO_RNAPol2Ser20821CR_DN_1
- GSM8968341 R1KO_RNAPol2Ser20905CR_DN_2
- GSM8968342 V1TxS_RNAPol2Ser20821CR_DN_1
- GSM8968343 V1TxS_RNAPol2Ser20905CR_DN_2
- GSM8968344 Misc_IgGcntrl0821CR_DN
- GSM8968345 Misc_IgGcntrl0905CR_DN
- GSM8968346 EbKO_H3K27ac10727CR_DN_1 EbKO_H3K27ac10727CR_DN
- GSM8968347 EbKO_H3K27ac10727CR_DN_2 EbKO_H3K27ac10727CR_DN
- GSM8968348 R1KO_H3K27ac0727CR_DN_1 R1KO_H3K27ac0727CR_DN
- GSM8968349 R1KO_H3K27ac0727CR_DN_2 R1KO_H3K27ac0727CR_DN
- GSM8968350 V1TxS_H3K27ac0724CR_DN_1
- GSM8968351 V1TxS_H3K27ac0727CR_DN_2
- GSM8968352 HTS_SO85_03_RCTKO_Nipbl1030CR_DN_1_S3
- GSM8968353 HTS_SO85_07_RCTKO_Nipbl1206CR_DN_2_S7
- GSM8968354 HTS_SO85_11_EbKO_Nipbl1206CR_DN_3_S11
- GSM8968355 HTS_SO85_21_EbKO_Nipbl1212CR_DN_4_S21
- GSM8968356 R1KO_Nipbl0816CR_DN_1 R1KO_Nipbl0816CR_DN
- GSM8968357 R1KO_Nipbl0816CR_DN_2 R1KO_Nipbl0816CR_DN
- GSM8968358 V1CScr_Nipbl0816CR_DN_1
- GSM8968359 V1CScr_Nipbl0821CR_DN_2
- GSM8968360 V1PKO_Nipbl0816CR_DN_1 V1PKO_Nipbl0816CR_DN
- GSM8968361 V1PKO_Nipbl0816CR_DN_2 V1PKO_Nipbl0816CR_DN
- GSM8968362 V1TxS_Nipbl0816CR_DN_1 V1TxS_Nipbl0816CR_DN
- GSM8968363 V1TxS_Nipbl0816CR_DN_2 V1TxS_Nipbl0816CR_DN
- GSM8968364 HTSSO52_V1TxS_Rad210712CR_DN_2
- GSM8968365 HTSSO57_V1TxS_Rad210712CR_DN_1
- GSM8968366 HTS_SO85_02_RCTKO_Rad211030CR_DN_1_S2
- GSM8968367 HTS_SO85_06_RCTKO_Rad211206CR_DN_2_S6
- GSM8968368 HTS_SO85_10_EbKO_Rad211206CR_DN_3_S10
- GSM8968369 HTS_SO85_20_EbKO_Rad211212CR_DN_4_S20
- GSM8968370 R1KO_Rad210712CR_DN_1 R1KO_Rad210712CR_DN
- GSM8968371 R1KO_Rad210712CR_DN_2 R1KO_Rad210712CR_DN
+ 41 more — browse all 81 samples with per-sample file links →
- GSE296314 Promoter- and Enhancer-Dependent Cohesin Loading Initiates Chromosome Looping to Fold Tcrb Loci for Long-Range Recombination [RNA-Seq] 16 samples shares enhancer-dependent, recombination, chromosome, long-range, initiates, promoter, cohesin, loading
- GSE339369 Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome 245 samples shares chromosome, promoter
- GSE262343 Principles of chromosome organization for meiotic recombination 65 samples shares recombination, chromosome
- GSE295769 Context-dependent regulation of IgH V(D)J recombination by cohesin-STAG1 and cohesin-STAG2 [ChIP-seq] 47 samples shares recombination, cohesin
- GSE339197 Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome [Regulators_KD_CutnTag] 44 samples shares chromosome, promoter
- GSE339202 Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome [Xist-Tsix-perturbations_CutnTag] 42 samples shares chromosome, promoter
- GSE288455 Unraveling the cohesin-chromatin interface: identifying protein interactions that modulate chromosome structure and function [ChIP-Seq] 22 samples shares chromosome, cohesin
- GSE339196 Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome [TX-Maged1-2tag_CutnTag] 12 samples shares chromosome, promoter
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.