CTCF regulates global chromatin accessibility and transcription during rod photoreceptor development
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: 8 × RNA-seq_control vs 8 × ATAC-seq_control vs 3 × RNA-seq_KO vs 3 × ATAC-seq_KOGroups 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 regulates global chromatin accessibility and transcription during rod photoreceptor developmentProceedings of the National Academy of Sciences of the United States of America · 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 GSE269683_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 PRJNA1123222 and SRA study SRP513537. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 22 samples.
How we read this: 4 replicated groups read from 26 sample titles; they account for 22 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.
- GSM8324588 RNA-seq_control_1 RNA-seq_control
- GSM8324589 RNA-seq_control_2 RNA-seq_control
- GSM8324590 RNA-seq_control_3 RNA-seq_control
- GSM8324591 RNA-seq_control_4 RNA-seq_control
- GSM8324592 RNA-seq_control_5 RNA-seq_control
- GSM8324593 RNA-seq_control_6 RNA-seq_control
- GSM8324594 RNA-seq_control_7 RNA-seq_control
- GSM8324595 RNA-seq_control_8 RNA-seq_control
- GSM8324596 RNA-seq_KO_1 RNA-seq_KO
- GSM8324597 RNA-seq_KO_2 RNA-seq_KO
- GSM8324598 RNA-seq_KO_3 RNA-seq_KO
- GSM8324599 ATAC-seq_control_1 ATAC-seq_control
- GSM8324600 ATAC-seq_control_2 ATAC-seq_control
- GSM8324601 ATAC-seq_control_3 ATAC-seq_control
- GSM8324602 ATAC-seq_control_4 ATAC-seq_control
- GSM8324603 ATAC-seq_control_5 ATAC-seq_control
- GSM8324604 ATAC-seq_control_6 ATAC-seq_control
- GSM8324605 ATAC-seq_control_7 ATAC-seq_control
- GSM8324606 ATAC-seq_control_8 ATAC-seq_control
- GSM8324607 ATAC-seq_KO_1 ATAC-seq_KO
- GSM8324608 ATAC-seq_KO_2 ATAC-seq_KO
- GSM8324609 ATAC-seq_KO_3 ATAC-seq_KO
- GSM8324610 CUT&Tag_CTCF
- GSM8324611 CUT&Tag_H3K27ac
- GSM8324612 CUT&Tag_H3K27me3
- GSM8324613 CUT&Tag_H3K4me1
- GSE274040 Transcriptional and chromatin accessibility landscapes of hematopoiesis in a mouse model of breast cancer 16 samples shares accessibility, transcription, chromatin
- GSE262521 Disentangling the architectural and non-architectural functions of CTCF and cohesin in global gene regulation 68 samples shares ctcf, global
- GSE234251 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [Mnase-seq] 21 samples shares ctcf, accessibility
- GSE283483 Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression programs in the hippocampus 160 samples shares accessibility, chromatin
- 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 transcription, chromatin
- GSE237534 INO80 / SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape 217 samples shares transcription, chromatin
- GSE200323 Establishment of chromatin architecture interplays with embryo hypertranscription 158 samples shares transcription, chromatin
- GSE294772 Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging [snATAC-Seq] [10X Multiome] 142 samples shares transcription, chromatin
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.