Dynamic Foxp3-chromatin interaction controls tunable Treg cell function [RNA-seq]
RNA-seq (gene expression) · mouse · 16 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 16 samples: 2 × RNA-aTe vs 2 × RNA-aTreg vs 2 × RNA-nT vs 2 × RNA-rTregGroups 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 GSE149693_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA629759 and SRA study SRP259916. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 16 sample titles; they account for 8 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.
- 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 RNA-aTe
- GSM4509070 RNA-aTe2 RNA-aTe
- GSM4509071 RNA-aTreg1 RNA-aTreg
- GSM4509072 RNA-aTreg2 RNA-aTreg
- GSM4509073 RNA-nT1 RNA-nT
- GSM4509074 RNA-nT2 RNA-nT
- GSM4509075 RNA-rTreg1 RNA-rTreg
- GSM4509076 RNA-rTreg2 RNA-rTreg
- GSE149674 Dynamic Foxp3-chromatin interaction controls tunable Treg cell function 94 samples shares foxp3-chromatin, interaction, controls, dynamic, tunable, treg
- GSE296993 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [RNA-seq of mESC] 50 samples shares dynamic, rna-seq
- GSE280373 Spatiotemporal dynamics of the cardioimmune niche during lesion repair [scRNA-seq] 28 samples shares dynamic, rna-seq
- GSE237783 Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages [RNA-Seq] 28 samples shares interaction, rna-seq
- GSE296992 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [RNA-seq of early embryo] 26 samples shares dynamic, rna-seq
- GSE310620 RNA-seq in aortic smooth muscle cells from a mice lacking Arg1 expression in erytrhrocytes (RBC.ARG1-KO) and their litter mate controls (RBC.ARG1-WT) after culture in standard DMEM or foam cell medium (DIAM) 16 samples shares controls, rna-seq
- GSE303460 Spatiotemporal single-cell atlas of suture stem cell dynamics in craniosynostosis [scRNA-Seq] 14 samples shares dynamic, rna-seq
- GSE277228 Changing dynamics of the fibroblast differentiation hierarchy during mammary gland morphogenesis and tumorigenesis [scRNA-Seq I] 13 samples shares dynamic, rna-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.