Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [RNA-seq]
RNA-seq (gene expression) · mouse · 35 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
- 35 samples: 10 conditions, mostly in triplicateGroups 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
- Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiationNature communications · 2025
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 GSE267441_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 PRJNA1111521 and SRA study SRP507613. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 35 samples.
How we read this: 10 replicated groups read from 35 sample titles; they account for 35 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.
- GSM8266812 t1_0h_rep1 t1_0h
- GSM8266813 t1_0h_rep2 t1_0h
- GSM8266814 t1_0h_rep3 t1_0h
- GSM8266815 t2_16h_rep1 t2_16h
- GSM8266816 t2_16h_rep2 t2_16h
- GSM8266817 t2_16h_rep3 t2_16h
- GSM8266818 t3_24h_rep1 t3_24h
- GSM8266819 t3_24h_rep2 t3_24h
- GSM8266820 t3_24h_rep3 t3_24h
- GSM8266821 t4_48h_rep1 t4_48h
- GSM8266822 t4_48h_rep2 t4_48h
- GSM8266823 t4_48h_rep3 t4_48h
- GSM8266824 t5_72h_rep1 t5_72h
- GSM8266825 t5_72h_rep2 t5_72h
- GSM8266826 t5_72h_rep3 t5_72h
- GSM8266827 t6_96h_rep1 t6_96h
- GSM8266828 t6_96h_rep2 t6_96h
- GSM8266829 t6_96h_rep3 t6_96h
- GSM8266830 t7_168h_rep1 t7_168h
- GSM8266831 t7_168h_rep2 t7_168h
- GSM8266832 t7_168h_rep3 t7_168h
- GSM8266833 t8_xen_rep1 t8_xen
- GSM8266834 t8_xen_rep2 t8_xen
- GSM9148206 siCTL_48h_1 siCTL_48h
- GSM9148207 siCTL_48h_2 siCTL_48h
- GSM9148208 siOct4_48h_1 siOct4_48h
- GSM9148209 siOct4_48h_2 siOct4_48h
- GSM9148210 siCTL_48h_3 siCTL_48h
- GSM9148211 siCTL_48h_4 siCTL_48h
- GSM9148212 siOct4_48h_3 siOct4_48h
- GSM9148213 siOct4_48h_4 siOct4_48h
- GSM9148214 siCTL_48h_5 siCTL_48h
- GSM9148215 siCTL_48h_6 siCTL_48h
- GSM9148216 siOct4_48h_5 siOct4_48h
- GSM9148217 siOct4_48h_6 siOct4_48h
- GSE282096 Diminished transcriptional activity and splicing changes drive gene length-biased rewiring in the aging transcriptome (RNA-Seq) 94 samples shares transcription, rna-seq
- GSE281037 Large-scale transcriptomic analyses reveal downstream target genes of ZFY1 and ZFY2 transcription factors in male germ cells 48 samples shares transcription, factors
- GSE248585 A conserved epithelial wound-like transcriptional program driven by FOSL1 underlies malignant progression of pancreatic ductal adenocarcinoma (ssRNA-Seq) 46 samples shares transcription, rna-seq
- GSE229238 DNA methylation constrains nucleosome retention in sperm and H3K4 methylation deposition in early mouse embryos [RNA-seq 2] 42 samples shares nucleosome, rna-seq
- GSE150817 Transcriptional dynamics of the murine heart during perinatal development at single-cell resolution 30 samples shares transcription, dynamics
- GSE245648 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [RNA-seq_BMDM] 24 samples shares transcription, rna-seq
- GSE245838 Anchored screening identifies transcription factor blueprints underlying dendritic cell diversity and subset-specific anti-tumor immunity [mouse scRNA-seq] 21 samples shares transcription, rna-seq
- GSE301186 Transcriptional and functional architecture of the whole neutrophil compartment [RNA-seq sorted_cells] 11 samples shares transcription, 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.