FoxO transcription factors actuate the formative pluripotency specific gene expression programme
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 66 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
- 66 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
- FoxO transcription factors actuate the formative pluripotency specific gene expression programmeNature communications · 2024
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 GSE253480_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 PRJNA1065862 and SRA study SRP484258. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 34 samples.
How we read this: 16 replicated groups read from 66 sample titles; they account for 34 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.
- GSM8021204 WT 2i, rep1 WT 2i,
- GSM8021205 WT 2i, rep2 WT 2i,
- GSM8021206 Pten KO 2i, rep1 Pten KO 2i,
- GSM8021207 Pten KO 2i, rep2 Pten KO 2i,
- GSM8021208 WT N24, rep1 WT N24,
- GSM8021209 WT N24, rep2 WT N24,
- GSM8021210 Pten KO N24, rep1 Pten KO N24,
- GSM8021211 Pten KO N24, rep2 Pten KO N24,
- GSM8021212 WT, N24, DMSO, rep1 WT, N24, DMSO,
- GSM8021213 Pten KO, N24, DMSO, rep1 Pten KO, N24, DMSO,
- GSM8021214 Tsc2 KO, N24, DMSO, rep1 Tsc2 KO, N24, DMSO,
- GSM8021215 WT, N24, Rapa, rep1 WT, N24, Rapa,
- GSM8021216 Pten KO, N24, Rapa, rep1 Pten KO, N24, Rapa,
- GSM8021217 Tsc2 KO, N24, Rapa, rep1 Tsc2 KO, N24, Rapa,
- GSM8021218 WT, N24, DMSO, rep2 WT, N24, DMSO,
- GSM8021219 Pten KO, N24, DMSO, rep2 Pten KO, N24, DMSO,
- GSM8021220 Tsc2 KO, N24, DMSO, rep2 Tsc2 KO, N24, DMSO,
- GSM8021221 WT, N24, Rapa, rep2 WT, N24, Rapa,
- GSM8021222 Pten KO, N24, Rapa, rep2 Pten KO, N24, Rapa,
- GSM8021223 Tsc2 KO, N24, Rapa, rep2 Tsc2 KO, N24, Rapa,
- GSM8021224 WT, N24, siCtrl, rep1 WT, N24, siCtrl,
- GSM8021225 WT, N24, siCtrl, rep2 WT, N24, siCtrl,
- GSM8021226 WT, N24, siCtrl, rep3 WT, N24, siCtrl,
- GSM8021227 WT, N24, siFoxo1, rep1 WT, N24, siFoxo1,
- GSM8021228 WT, N24, siFoxo1, rep2 WT, N24, siFoxo1,
- GSM8021229 WT, N24, siFoxo1, rep3 WT, N24, siFoxo1,
- GSM8021230 WT, 2i, rep1 WT, 2i,
- GSM8021231 WT, 2i, rep2 WT, 2i,
- GSM8021232 WT, 2i, MK, rep1 WT, 2i, MK,
- GSM8021233 WT, 2i, MK, rep2 WT, 2i, MK,
- GSM8021234 WT, N24, rep1 WT, N24,
- GSM8021235 WT, N24, rep2 WT, N24,
- GSM8021236 WT, N24, MK, rep1 WT, N24, MK,
- GSM8021237 WT, N24, MK, rep2 WT, N24, MK,
- GSM8021392 FoxO1, WT 2i, rep1, input
- GSM8021393 FoxO1, Pten KO 2i, rep1, input
- GSM8021394 FoxO1, WT 2i, rep2, input
- GSM8021395 FoxO1, Pten KO 2i, rep2, input
- GSM8021396 FoxO1, WT N24, rep1, input
- GSM8021397 FoxO1, Pten KO N24, rep1, input
+ 26 more — browse all 66 samples with per-sample file links →
- GSE270036 Investigate the functions of core pluripotency transcription factors in embryonic stem cells 30 samples shares transcription, pluripotency, factors
- GSE282280 DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation. 93 samples shares transcription, factors
- GSE267584 Enhancer-driven gene regulatory networks reveal transcription factors governing T cell adaptation and differentiation in the tumor microenvironment. 22 samples shares transcription, factors
- GSE288339 Postmitotic transcription and 3D regulation show locus-specific and differentiation-specific sensitivity to cohesin depletion 109 samples shares transcription, specific
- GSE283382 N6-methyladenosine modulate second cell fate decision by enhancing mRNA stability of pivotal transcription factors during primitive endoderm development [TBLC_RNAseq] 98 samples shares transcription, factors
- GSE281037 Large-scale transcriptomic analyses reveal downstream target genes of ZFY1 and ZFY2 transcription factors in male germ cells 48 samples shares transcription, factors
- GSE310057 A RiboCancer cell line panel reveals that CLL-associated Rps15 mutations translationally rewire transcription through codon-specific tRNA accommodation defects 48 samples shares transcription, specific
- GSE283958 Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators 47 samples shares transcription, factors
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.