Dynamic Foxp3-chromatin interaction controls tunable Treg cell function
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 94 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
- 94 samples: 84 distinct titles, 8 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
- 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 GSE149674_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 PRJNA629580 and SRA study SRP259375. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 94 sample titles: 84 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.
- GSM4508695 1436476_Foxp3_PSI_1
- GSM4508696 1436477_Foxp3_PSI_2
- GSM4508697 1436478_Foxp3_PSI_3
- GSM4508698 1484803_Foxp3_Traditional
- GSM4508699 ATAC-YF_T-iTr-AA2P Replicate 1
- GSM4508700 ATAC-YF_T-iTr-AA2P Replicate 2
- GSM4508701 ATAC-YF_Tr Replicate 1
- GSM4508702 ATAC-YF_Tr Replicate 2
- GSM4509061 RNA-1835231_minusIL2a
- GSM4509062 RNA-1835232_minusIL2b
- GSM4509063 RNA-1835233_plusIL2a
- GSM4509064 RNA-1835234_plusIL2b
- GSM4509065 RNA-1835235_minusTCRa
- GSM4509066 RNA-1835236_minusTCRb
- GSM4509067 RNA-1835237_plusTCRa
- GSM4509068 RNA-1835238_plusTCRb
- GSM4509069 RNA-aTe1
- GSM4509070 RNA-aTe2
- GSM4509071 RNA-aTreg1
- GSM4509072 RNA-aTreg2
- GSM4509073 RNA-nT1
- GSM4509074 RNA-nT2
- GSM4509075 RNA-rTreg1
- GSM4509076 RNA-rTreg2
- GSM7836301 2571416_ATACseq_TCR_NC1
- GSM7836302 2571417_ATACseq_TCR_NC2
- GSM7836303 2571420_ATACseq_TCR_sgBatf1
- GSM7836304 2571421_ATACseq_TCR_sgBatf2
- GSM7836305 ATreg_WT_Rep1
- GSM7836306 ATreg_WT_Rep2
- GSM7836307 ATreg_WT_Rep3
- GSM7836308 RTreg_WT_Rep1
- GSM7836309 RTreg_WT_Rep2
- GSM7836310 RTreg_WT_Rep3
- GSM7836311 2512250_RNAseq_TCR0h_NC_1
- GSM7836312 2512251_RNAseq_TCR0h_NC_2
- GSM7836313 2512252_RNAseq_TCR3h_NC_1
- GSM7836314 2512253_RNAseq_TCR3h_NC_2
- GSM7836315 2512254_RNAseq_TCR0h_sgFoxp3_1
- GSM7836316 2512255_RNAseq_TCR0h_sgFoxp3_2
+ 54 more — browse all 94 samples with per-sample file links →
- GSE316171 Fibroblast Growth Factor Receptor Signaling in Maturing Osteoblasts Controls Cell-Matrix Interactions Critical for Osteocyte Survival 8 samples shares interaction, controls
- GSE252269 Targeting the FOXP3–T-bet interaction to restore Treg stability in IFN-γ–driven autoimmunity [CUT&Tag/ATAC-seq] 18 samples shares interaction, treg
- GSE254162 Dynamic fibroblast-immune interactions shape recovery after brain injury [snRNASeq_Timecourse] 12 samples shares interaction, dynamic
- GSE261250 Gfi1 controls the formation of effector CD8+ T cells during chronic infection and cancer 47 samples shares controls
- GSE329967 Temporal Single-Cell Transcriptional Dynamics of Murine Pancreatic Islet Remodeling During Hyperglycaemia Progression 33 samples shares dynamic
- GSE331488 A global view of cell-type-specific temporal dynamics in mammalian aging [I] 771 samples shares dynamic
- GSE255212 Transcriptomic Signatures of WNT-Driven Pathways and Granulosa Cell-Oocyte Interaction during Primordial Follicle Activation 762 samples shares interaction
- GSE331489 A global view of cell-type-specific temporal dynamics in mammalian aging [II] 725 samples shares dynamic
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.