ATAC-seq analysis of early T cell progenitors from various gene deficient mice
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- 12 samples: 6 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
- A feedback amplifier circuit with Notch and E2A orchestrates T-cell fate and suppresses the innate lymphoid cell lineages during thymic ontogenyGenes & development · 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 GSE245399_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 PRJNA1028279 and SRA study SRP466402. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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.
- GSM7842068 ATAC-B6-ETP-1 ATAC-B6-ETP
- GSM7842069 ATAC-B6-ETP-2 ATAC-B6-ETP
- GSM7842070 ATAC-E47KO-ETP-1 ATAC-E47KO-ETP
- GSM7842071 ATAC-E47KO-ETP-2 ATAC-E47KO-ETP
- GSM7842072 ATAC-N1En_del-ETP-1 ATAC-N1En_del-ETP
- GSM7842073 ATAC-N1En_del-ETP-2 ATAC-N1En_del-ETP
- GSM7842074 ATAC-N1En_del-E47KO-ETP-1 ATAC-N1En_del-E47KO-ETP
- GSM7842075 ATAC-N1En_del-E47KO-ETP-2 ATAC-N1En_del-E47KO-ETP
- GSM7842076 ATAC-E2A/HEB-dKO-ETP-1 ATAC-E2A/HEB-dKO-ETP
- GSM7842077 ATAC-E2A/HEB-dKO-ETP-2 ATAC-E2A/HEB-dKO-ETP
- GSM7842078 ATAC-E2A/HEB-dKO_NICD-ETP-1 ATAC-E2A/HEB-dKO_NICD-E…
- GSM7842079 ATAC-E2A/HEB-dKO_NICD-ETP-2 ATAC-E2A/HEB-dKO_NICD-E…
- GSE264614 Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in mouse early embryos [ATAC-seq] 44 samples shares atac-seq, early
- GSE245683 ATAC-seq of mouse cortex undergoing early degradation after traumatic brain injury (TBI) 12 samples shares atac-seq, early
- GSE271884 GFI1-driven transcriptional and epigenetic programs maintain memory CD8+ T cell persistence [ATAC-seq]. 30 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
- GSE286574 Intrauterine hyperglycemia impairs primordial germ cell development and fertility by sex-specific epigenetic reprogramming interference in mice offspring [ATAC-seq] 30 samples shares atac-seq
- GSE283255 Distinct Vps34-orchestrated signaling processes dictate the transitional heterogeneity and functional adaptation of effector Treg cells [ATAC-seq2] 14 samples shares atac-seq
- GSE283256 Distinct Vps34-orchestrated signaling processes dictate the transitional heterogeneity and functional adaptation of effector Treg cells [ATAC-seq1] 10 samples shares atac-seq
- GSE279088 Molecular dynamics driving phenotypic divergence among KRAS mutants in pancreatic tumorigenesis [ATAC-Seq] 74 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.