Dynamic Foxp3-chromatin interaction controls tunable Treg cell function [Cut&Run Foxp3 Batf]
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: 12 samples, each with a distinct title — no replicated groupsGroups 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
- Dynamic Foxp3-chromatin interaction controls tunable Treg cell functionThe Journal of experimental medicine · 2024
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 GSE245100_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 PRJNA1026939 and SRA study SRP465849. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 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.
- GSM7836319 2523655_CR_Batf_rTreg_1
- GSM7836320 2523656_CR_Batf_rTreg_2
- GSM7836321 2523657_CR_Batf_aTreg_1
- GSM7836322 2523658_CR_Batf_aTreg_2
- GSM7836323 2570658_aFoxp3_CR_TCR_NC1
- GSM7836324 2570659_aFoxp3_CR_TCR_NC2
- GSM7836325 2570662_aFoxp3_CR_TCR_sgBatf1
- GSM7836326 2570663_aFoxp3_CR_TCR_sgBatf2
- GSM7836327 2580184_aBatf_NC_TCR_1
- GSM7836328 2580185_aBatf_NC_TCR_2
- GSM7836329 2580188_aBatf_sgBatf_TCR_1
- GSM7836330 2580189_aBatf_sgBatf_TCR_2
- GSE268623 Dynamic Foxp3-chromatin interaction controls tunable Treg cell function [Cut&Run Foxp3 Batf Ets1] 24 samples shares foxp3, foxp3-chromatin, interaction, controls, dynamic, tunable, treg, batf
- GSE149674 Dynamic Foxp3-chromatin interaction controls tunable Treg cell function 94 samples shares foxp3, foxp3-chromatin, interaction, controls, dynamic, tunable, treg
- GSE267882 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [ChIP-Seq] 34 samples shares foxp3, treg, batf
- GSE267881 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [ATAC-Seq] 30 samples shares foxp3, treg, batf
- GSE252269 Targeting the FOXP3–T-bet interaction to restore Treg stability in IFN-γ–driven autoimmunity [CUT&Tag/ATAC-seq] 18 samples shares foxp3, interaction, treg
- GSE267967 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for functional differentiation of Treg cells [RNA-seq] 26 samples shares foxp3, treg, batf
- GSE267884 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [scMultiome] 16 samples shares foxp3, treg, batf
- GSE311963 CD38 endows local antigen-specific Foxp3+ Treg cells with stress resilience for compartmentalized control of CNS inflammation 68 samples shares foxp3, treg
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.