CTCF tunes gene expression in a loop-dependent and -independent manner [RNA-seq]
RNA-seq (gene expression) · mouse · 32 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 32 samples: 16 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's loop-independent functions prevail over chromatin looping in the acute degradation systemProtein & cell · 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 GSE274773_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1147848 and SRA study SRP526227. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 32 samples.
How we read this: 16 replicated groups read from 32 sample titles; they account for 32 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.
- GSM8457622 CTCF_AID_0h_rep1 CTCF_AID_0h
- GSM8457623 CTCF_AID_0h_rep2 CTCF_AID_0h
- GSM8457624 CTCF_AID_12h_rep1 CTCF_AID_12h
- GSM8457625 CTCF_AID_12h_rep2 CTCF_AID_12h
- GSM8457626 CTCF_AID_24h_rep1 CTCF_AID_24h
- GSM8457627 CTCF_AID_24h_rep2 CTCF_AID_24h
- GSM8457628 RAD21_AID_0h_rep1 RAD21_AID_0h
- GSM8457629 RAD21_AID_0h_rep2 RAD21_AID_0h
- GSM8457630 RAD21_AID_12h_rep1 RAD21_AID_12h
- GSM8457631 RAD21_AID_12h_rep2 RAD21_AID_12h
- GSM8457632 RAD21_AID_24h_rep1 RAD21_AID_24h
- GSM8457633 RAD21_AID_24h_rep2 RAD21_AID_24h
- GSM8457634 oectrl_rep1 oectrl
- GSM8457635 oectrl_rep2 oectrl
- GSM8457636 oectrl_IAA_rep1 oectrl_IAA
- GSM8457637 oectrl_IAA_rep2 oectrl_IAA
- GSM8457638 oeCTCFwt_rep1 oeCTCFwt
- GSM8457639 oeCTCFwt_rep2 oeCTCFwt
- GSM8457640 oeCTCFmut_rep1 oeCTCFmut
- GSM8457641 oeCTCFmut_rep2 oeCTCFmut
- GSM8457642 oeCTCFwt_IAA_rep1 oeCTCFwt_IAA
- GSM8457643 oeCTCFwt_IAA_rep2 oeCTCFwt_IAA
- GSM8457644 oeCTCFmut_IAA_rep1 oeCTCFmut_IAA
- GSM8457645 oeCTCFmut_IAA_rep2 oeCTCFmut_IAA
- GSM9161142 CTCF_AID_0h_serum_rep1 CTCF_AID_0h_serum
- GSM9161143 CTCF_AID_0h_serum_rep2 CTCF_AID_0h_serum
- GSM9161144 CTCF_AID_12h_serum_rep1 CTCF_AID_12h_serum
- GSM9161145 CTCF_AID_12h_serum_rep2 CTCF_AID_12h_serum
- GSM9161146 shctrl_rep1 shctrl
- GSM9161147 shctrl_rep2 shctrl
- GSM9161148 shChd4_rep1 shChd4
- GSM9161149 shChd4_rep2 shChd4
- GSE262521 Disentangling the architectural and non-architectural functions of CTCF and cohesin in global gene regulation 68 samples shares ctcf
- GSE267967 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for functional differentiation of Treg cells [RNA-seq] 26 samples shares rna-seq
- GSE264105 Plate-based scRNA-seq of plasma-positive microglia and plasma-negative microglia in young mice 1111 samples shares rna-seq
- GSE263415 Spatial hepatocyte plasticity of gluconeogenic gene expression and gluconeogenic activity during the metabolic transitions between fed, fasted and starvation states [RNA-Seq] 18 samples shares rna-seq
- GSE328496 Gene expression + ATAC profiling of trisomic hippocampal neurons upon SAHA treatment [RNA-seq] 16 samples shares rna-seq
- GSE326100 scRNA-seq of mouse cochlea organoid cells 768 samples shares rna-seq
- GSE311449 Single cell RNA-seq of mouse brain vascular cells with Smart-seq2 method 391 samples shares rna-seq
- GSE226579 Stem Cell Activity-Coupled Suppression of Endogenous Retrovirus Governs Adult Tissue Regeneration [RNA-seq] 47 samples shares rna-seq
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.