Chromatin-dependent motif syntax defines differentiation trajectories [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 22 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
- 22 samples: 20 distinct titles, 2 of them repeatedGroups 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
- Chromatin-dependent motif syntax defines differentiation trajectoriesMolecular cell · 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 GSE272529_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 PRJNA1137293 and SRA study SRP520754. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 22 sample titles: 20 distinct titles with little repetition. 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.
- GSM8404033 ATACseq_GFP_6h_r1_1854
- GSM8404034 ATACseq_GFP_6h_r2_1854
- GSM8404035 ATACseq_NGN2_6h_r1_1854
- GSM8404036 ATACseq_NGN2_6h_r2_1854
- GSM8404037 ATACseq_NGN2mut_6h_r1_1854
- GSM8404038 ATACseq_NGN2mut_6h_r2_1854
- GSM8404039 ATACseq_MYOD1_6h_r1_2028
- GSM8404040 ATACseq_MYOD1_6h_r2_2028
- GSM8404041 ATACseq_GFP_6h_r1_2028
- GSM8404042 ATACseq_GFP_6h_r2_2028
- GSM8404043 ATACseq_GFP_24h_r1_2276
- GSM8404044 ATACseq_GFP_24h_r2_2276
- GSM8404045 ATACseq_NGN_24h_r1_2276
- GSM8404046 ATACseq_NGN_24h_r2_2276
- GSM8404047 ATACseq_MYOD1_24h_r1_2276
- GSM8404048 ATACseq_MYOD1_24h_r2_2276
- GSM8404049 ATACseq_mESC_r1_1855
- GSM8404050 ATACseq_mESC_r2_1855
- GSM8404051 ATACseq_NGN2_24h_1855
- GSM8404052 ATACseq_NGN2mut_24h_1855
- GSM8404053 ATACseq_GFP_24h_1855
- GSM8404054 ATACseq_NGN2_ES24h_1855
- GSE272524 Chromatin-dependent motif syntax defines differentiation trajectories [ChIP-seq] 76 samples shares chromatin-dependent, trajectories, defines, syntax, motif
- GSE296200 A20’s Linear Ubiquitin Binding Motif Restrains Pathogenic Activation of TH17/22 cells and IL-22 Driven Enteritis [ATAC-seq] 11 samples shares atac-seq, motif
- GSE321762 Vascular smooth muscle cell state trajectories mediate molecular mechanisms of coronary disease risk [scRNA-seq and scATAC-seq] 54 samples shares trajectories, atac-seq
- GSE278157 A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells [ATAC-seq] 40 samples shares atac-seq
- GSE289298 OTX2 controls chromatin accessibility to direct somatic versus germline differentiation [ATAC-Seq] 32 samples shares atac-seq
- GSE267881 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [ATAC-Seq] 30 samples shares atac-seq
- GSE281498 The transcription factor BATF pioneers the differentiation program of cytolytic effector CD8+ T cells through the direct interaction with IRF4 (ATAC-seq) 20 samples shares atac-seq
- GSE309864 Modulating MyoD1 dosage activates alternate cell fate beyond myogenic differentiation [ATAC-seq] 16 samples shares atac-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.