The chromatin assembly factor CHAF1b functions as an epigenetic amplifier of RORγt to promote Th17 pathogenicity and autoimmunity
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 13 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
- 13 samples: 4 × Wild-type vs 3 × Wild-type, vs 3 × KO, vs 2 × KOGroups 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.
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 GSE326921_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 PRJNA1447944 and SRA study SRP689119. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 13 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.
- GSM9643604 RNA-seq of Th17 cells: Wild-type, biological replicate 1 Wild-type,
- GSM9643605 RNA-seq of Th17 cells: Wild-type, biological replicate 2 Wild-type,
- GSM9643606 RNA-seq of Th17 cells: Wild-type, biological replicate 3 Wild-type,
- GSM9643607 RNA-seq of Th17 cells: KO, biological replicate 1 KO,
- GSM9643608 RNA-seq of Th17 cells: KO, biological replicate 2 KO,
- GSM9643609 RNA-seq of Th17 cells: KO, biological replicate 3 KO,
- GSM9643610 H3K4me3 ChIP-seq of Th17 cells: Wild-type Wild-type
- GSM9643611 H3K4me3 ChIP-seq of Th17 cells: KO KO
- GSM9643612 Chaf1b ChIP-seq of Th17 cells: Wild-type Wild-type
- GSM9643613 ATAC-seq of Th17 cells: Wild-type Wild-type
- GSM9643614 ATAC-seq of Th17 cells: KO KO
- GSM9643615 RORgt CUT&Tag of Th17 cells: Wild-type Wild-type
- GSM9643616 RORgt CUT&Tag of Th17 cells: HO
- GSE298306 Immune-responsive gene-1: The mitochondrial Key to Th17 Cell Pathogenicity in CNS Autoimmunity 18 samples shares th17, pathogenicity, autoimmunity
- GSE284714 AMPK signaling downstream of adenosine 2A receptor represses Th17 cell pathogenicity through epigenetic and metabolic reprogramming. 15 samples shares th17, pathogenicity, epigenetic
- GSE233908 Transcription factor TCF1 binds Rorgt and orchestrates a regulatory network that determines homeostatic Th17 cell state 21 samples shares th17, ror
- GSE296401 Interleukin-23 promotes a pro-inflammatory Th17 cell state by stabilizing RORγt and suppressing glucocorticoid receptor activity II 38 samples shares th17, ror
- GSE233905 Transcription factor TCF1 binds Rorgt and orchestrates a regulatory network that determines homeostatic Th17 cell state [ATAC-seq] 13 samples shares th17, ror
- GSE295997 Developmentally dynamic chromatin state at loci regulating interorgan communication 96 samples shares ror, chromatin
- GSE310456 Adipose tissue-derived microRNAs as epigenetic modulators of type 2 diabetes [DPDR_RNASEQ] 30 samples shares ror, epigenetic
- GSE301448 Epigenetic Reactivation of CNS Endothelial Developmental Programs Triggers Adult Brain Angiogenesis, Promotes Post-Stroke Revascularization and Neuroregeneration [RNAseq-Stroke] 18 samples shares ror, epigenetic
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.