CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 26 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
- 26 samples: 12 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
- CTCF-mediated 3D chromatin predetermines the gene expression program in the male germlinebioRxiv : the preprint server for biology · 2023
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 GSE244681_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 PRJNA1024383 and SRA study SRP464680. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 26 samples.
How we read this: 12 replicated groups read from 26 sample titles; they account for 26 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.
- GSM7823632 CTCF_ChIP_THY1_WT_rep1 CTCF_ChIP_THY1_WT
- GSM7823633 CTCF_ChIP_THY1_WT_rep2 CTCF_ChIP_THY1_WT
- GSM7823634 CTCF_ChIP_PS_WT_rep1 CTCF_ChIP_PS_WT
- GSM7823635 CTCF_ChIP_PS_WT_rep2 CTCF_ChIP_PS_WT
- GSM7823636 CTCF_ChIP_PS_Scml2-KO_rep1 CTCF_ChIP_PS_Scml2-KO
- GSM7823637 CTCF_ChIP_PS_Scml2-KO_rep2 CTCF_ChIP_PS_Scml2-KO
- GSM7823638 Hi-C_THY1_WT_rep1 Hi-C_THY1_WT
- GSM7823639 Hi-C_THY1_WT_rep2 Hi-C_THY1_WT
- GSM7823640 Hi-C_KIT_WT_rep1 Hi-C_KIT_WT
- GSM7823641 Hi-C_KIT_WT_rep2 Hi-C_KIT_WT
- GSM7823642 Hi-C_PS_WT_rep1 Hi-C_PS_WT
- GSM7823643 Hi-C_PS_WT_rep2 Hi-C_PS_WT
- GSM7823644 Hi-C_RS_WT_rep1 Hi-C_RS_WT
- GSM7823645 Hi-C_RS_WT_rep2 Hi-C_RS_WT
- GSM7823646 Hi-C_PS_Scml2-KO_rep1 Hi-C_PS_Scml2-KO
- GSM7823647 Hi-C_PS_Scml2-KO_rep2 Hi-C_PS_Scml2-KO
- GSM7823648 Hi-C_RS_Scml2-KO_rep1 Hi-C_RS_Scml2-KO
- GSM7823649 Hi-C_RS_Scml2-KO_rep2 Hi-C_RS_Scml2-KO
- GSM7823650 Hi-C_PS_A-myb-KO_rep1 Hi-C_PS_A-myb-KO
- GSM7823651 Hi-C_PS_A-myb-KO_rep2 Hi-C_PS_A-myb-KO
- GSM8402193 RNAseq_PS_Amyb_Ctrl_rep1 RNAseq_PS_Amyb_Ctrl
- GSM8402194 RNAseq_PS_Amyb_Ctrl_rep2 RNAseq_PS_Amyb_Ctrl
- GSM8402195 RNAseq_PS_Amyb_Ctrl_rep3 RNAseq_PS_Amyb_Ctrl
- GSM8402196 RNAseq_PS_Amyb_KO_rep1 RNAseq_PS_Amyb_KO
- GSM8402197 RNAseq_PS_Amyb_KO_rep2 RNAseq_PS_Amyb_KO
- GSM8402198 RNAseq_PS_Amyb_KO_rep3 RNAseq_PS_Amyb_KO
- GSE283483 Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression programs in the hippocampus 160 samples shares chromatin, program
- GSE290224 Intermittent Fasting Reprograms Chromatin Accessibility to Modulate Gene Expression in Brain and Muscle 96 samples shares chromatin, program
- GSE204933 Age-associated chromatin reorganization drives overexpression of a novel Btaf1 variant regulating HSC self-renewal and MkP differentiation in male mice 82 samples shares chromatin, male
- GSE296438 Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at the promoters of genes expressed during meiosis [scRNA-seq & scATAC-seq] 10 samples shares chromatin, male
- GSE278100 Foxa1-Mediated Chromatin Remodeling and Enhancer Reprogramming Promotes Gemcitabine Resistance in Pancreatic Cancer 54 samples shares chromatin, program
- GSE241378 Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of embryonic stem cell maintenance and neuronal differentiation. 36 samples shares chromatin, program
- GSE264229 Mapping the male mouse chromatin accessibility landscape by UUATAC-seq 33 samples shares chromatin, male
- GSE295991 Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at meiotic promoters in mice 32 samples shares chromatin, male
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.