Context-dependent regulation of IgH V(D)J recombination by cohesin-STAG1 and cohesin-STAG2 [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 47 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
- 47 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
- Context-dependent regulation of IgH V(D)J recombination by cohesin-STAG1 and cohesin-STAG2Nature communications · 2026
Read the full summary ↓
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 GSE295769_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 PRJNA1256334 and SRA study SRP581942. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 47 samples.
How we read this: 20 replicated groups read from 47 sample titles; they account for 47 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.
- GSM8957051 IP_STAG2_WT_rep1 IP_STAG2_WT
- GSM8957052 IP_STAG2_WT_rep2 IP_STAG2_WT
- GSM8957053 IP_STAG2_Stag1KO_rep1 IP_STAG2_Stag1KO
- GSM8957054 IP_STAG2_Stag1KO_rep2 IP_STAG2_Stag1KO
- GSM8957055 IP_STAG2_Stag2KO_rep1 IP_STAG2_Stag2KO
- GSM8957056 IP_STAG2_Stag2KO_rep2 IP_STAG2_Stag2KO
- GSM8957057 IP_SMC3_WT_rep1 IP_SMC3_WT
- GSM8957058 IP_SMC3_WT_rep2 IP_SMC3_WT
- GSM8957059 IP_SMC3_Stag1KO_rep1 IP_SMC3_Stag1KO
- GSM8957060 IP_SMC3_Stag1KO_rep2 IP_SMC3_Stag1KO
- GSM8957061 IP_SMC3_Stag2KO_rep1 IP_SMC3_Stag2KO
- GSM8957062 IP_SMC3_Stag2KO_rep2 IP_SMC3_Stag2KO
- GSM8957063 IP_CTCF_WT_rep1 IP_CTCF_WT
- GSM8957064 IP_CTCF_WT_rep2 IP_CTCF_WT
- GSM8957065 IP_CTCF_CTCF-Nm_rep1 IP_CTCF_CTCF-Nm
- GSM8957066 IP_CTCF_CTCF-Nm_rep2 IP_CTCF_CTCF-Nm
- GSM8957067 IP_SMC3_WT_rep3 IP_SMC3_WT
- GSM8957068 IP_SMC3_WT_rep4 IP_SMC3_WT
- GSM8957069 IP_SMC3_CTCF-Nm_rep1 IP_SMC3_CTCF-Nm
- GSM8957070 IP_SMC3_CTCF-Nm_rep2 IP_SMC3_CTCF-Nm
- GSM8957076 IP_STAG1_Stag2KO_CTCF-Nm_rep1 IP_STAG1_Stag2KO_CTCF-Nm
- GSM8957077 IP_STAG1_Stag2KO_CTCF-Nm_rep2 IP_STAG1_Stag2KO_CTCF-Nm
- GSM8957078 Input_WT_rep1 Input_WT
- GSM8957079 Input_WT_rep2 Input_WT
- GSM8957080 Input_Stag1KO_rep1 Input_Stag1KO
- GSM8957081 Input_Stag1KO_rep2 Input_Stag1KO
- GSM8957082 Input_Stag2KO_rep1 Input_Stag2KO
- GSM8957083 Input_Stag2KO_rep2 Input_Stag2KO
- GSM8957084 Input_CTCF-Nm_rep1 Input_CTCF-Nm
- GSM8957085 Input_CTCF-Nm_rep2 Input_CTCF-Nm
- GSM8957086 Input_Stag2KO_CTCF-Nm_rep1 Input_Stag2KO_CTCF-Nm
- GSM8957087 Input_Stag2KO_CTCF-Nm_rep2 Input_Stag2KO_CTCF-Nm
- GSM9263142 IP_STAG1_WT_rep1 IP_STAG1_WT
- GSM9263143 IP_STAG1_WT_rep2 IP_STAG1_WT
- GSM9263144 IP_STAG1_Stag1KO_rep1 IP_STAG1_Stag1KO
- GSM9263145 IP_STAG1_Stag1KO_rep2 IP_STAG1_Stag1KO
- GSM9263146 IP_STAG1_Stag2KO_rep1 IP_STAG1_Stag2KO
- GSM9263147 IP_STAG1_Stag2KO_rep2 IP_STAG1_Stag2KO
- GSM9263148 IP_STAG1_Stag2KO_rep3 IP_STAG1_Stag2KO
- GSM9549764 IP_STAG1_WT_rep5 IP_STAG1_WT
+ 7 more — browse all 47 samples with per-sample file links →
- GSE312228 Stag2-mediated chromatin dynamics regulates antibody class switch recombination [ChIP-Seq] 17 samples shares recombination, chip-seq
- GSE299391 Chromatin-intrinsic mechanisms determine orientation-specific class switch recombination [ChIP-Seq] 8 samples shares recombination, chip-seq
- GSE296303 Promoter- and Enhancer-Dependent Cohesin Loading Initiates Chromosome Looping to Fold Tcrb Loci for Long-Range Recombination [ChIP-Seq] 8 samples shares recombination, chip-seq
- GSE270088 53BP1 orchestrates sequence feature of RAG targets to balance DNA repair outcomes during V(D)J recombination [ChIP-seq] 4 samples shares recombination, chip-seq
- GSE262343 Principles of chromosome organization for meiotic recombination 65 samples shares recombination
- GSE296305 Promoter- and Enhancer-Dependent Cohesin Loading Initiates Chromosome Looping to Fold Tcrb Loci for Long-Range Recombination [CUT&RUN] 42 samples shares recombination
- GSE288585 Jk DNA GAGA MOTIFS ARE REQUIRED FOR LOCAL NUCLEOSOME REMODELING AND Vk-Jk RECOMBINATION [ATAC-Seq] 27 samples shares recombination
- GSE297597 Temporal and Context-Dependent Requirements for the Transcription Factor Foxp3 in Regulatory T Cell Development and Maintenance [ATAC_bulk_adult] 14 samples shares context-dependent
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.