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SATB1 Lowers The TCR Signaling Threshold For Thymocytes Positive Selection via Super-enhancer Reprogramming

GSE313769 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 122 samples Submitted 2025/12/19 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 122 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
122 samples: 39 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.
Summary (written by the submitters)
The generation of mature CD4⁺ helper and CD8⁺ cytotoxic T cells from double-positive (DP) thymocytes is a central step in building an effective adaptive immune system. This process relies on positive selection, whereby αβTCR⁺ thymocytes are tested for recognition of self-peptide–MHC complexes presented by cortical thymic epithelial cells.
Read the full summary ↓
Thymocytes with insufficient signaling die by neglect, while those receiving appropriately tuned signals survive and differentiate. Positive selection thus plays a dual role: establishing MHC restriction and directing lineage commitment into the CD4 or CD8 fate. After TCR rearrangement is completed, T cells can interact with APCs to transmit TCR signals and produce CD69 protein. SO, CD69+DP cells is undergoing positive selection. Here, we explored the mechanism of SATB1 regulating thymocyte positive selection. Firstly, We analysis the function of SATB1 in the transtion of CD69-DP to CD69+DP by CUT&Tag, ATAC and HiC assays. Then, Single-cell RNA sequencing assay of SATB1-deficient thymocytes showed that the cell identity of CD69+DP thymocytes was changed, and the genes differently expressed in CD69+DP cells. Smart-seq2 showed the similar tendency. CUT&Tag , ATAC-seq and HiC data show the mechanism for SATB1 in T cell positive selection or before this stage. ACC-seq confirms that SATB1 forms phase separation at these sites and regulates gene expression, These data helps us to understand the role of SATB1 in thymocyte positive selection.
This dataset
Open GSE313769 in finder → Find more mouse ChIP / ATAC / CUT&Tag datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE313769_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1381568 and SRA study SRP655292. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
39 conditions, mostly in triplicate
CD69+DP-Satb1KO-HIC ×4 CD69+DP-Satb1WT-HIC ×4 CD69-DP-Satb1KO-HIC ×4 CD69-DP-Satb1WT-HIC ×4 CD69-DP-Satb1WT-ATAC ×4 CD69+DP-Satb1WT-ATAC ×4 CD69-DP-Satb1KO-ATAC ×4 CD69+DP-Satb1KO-ATAC ×4 +32 more

Supports a between-group comparison across 121 samples.

How we read this: 39 replicated groups read from 122 sample titles; they account for 121 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.

Samples in this study

+ 82 more — browse all 122 samples with per-sample file links →

Datasets on a similar topic

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