Mechanism for controlled assembly of transcriptional condensates by Aire
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 75 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
- Homo sapiens (human)
- Samples
- 75 samples: 28 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.
- Paper
- Mechanism for controlled assembly of transcriptional condensates by AireNature immunology · 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 GSE243825_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 PRJNA1020110 and SRA study SRP462690. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 71 samples.
How we read this: 28 replicated groups read from 75 sample titles; they account for 71 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.
- GSM7796122 WT AIRE 4D6, no Dox ctrl, rep1 WT AIRE 4D6, no Dox ctr…
- GSM7796123 WT AIRE 4D6, no Dox ctrl, rep2 WT AIRE 4D6, no Dox ctr…
- GSM7796124 WT AIRE 4D6, Dox, rep1 WT AIRE 4D6, Dox,
- GSM7796125 WT AIRE 4D6, Dox, rep2 WT AIRE 4D6, Dox,
- GSM7796126 Day7_mKate2_Neg_rep1 Day7_mKate2_Neg
- GSM7796127 Day7_mKate2_Neg_rep2 Day7_mKate2_Neg
- GSM7796128 Day7_mKate2_Neg_rep3 Day7_mKate2_Neg
- GSM7796129 Day7_mKate2_Pos_rep1 Day7_mKate2_Pos
- GSM7796130 Day7_mKate2_Pos_rep2 Day7_mKate2_Pos
- GSM7796131 Day7_mKate2_Pos_rep3 Day7_mKate2_Pos
- GSM7796132 Day10_mKate2_Neg_rep1 Day10_mKate2_Neg
- GSM7796133 Day10_mKate2_Neg_rep2 Day10_mKate2_Neg
- GSM7796134 Day10_mKate2_Neg_rep3 Day10_mKate2_Neg
- GSM7796135 Day10_mKate2_Pos_rep1 Day10_mKate2_Pos
- GSM7796136 Day10_mKate2_Pos_rep2 Day10_mKate2_Pos
- GSM7796137 Day10_mKate2_Pos_rep3 Day10_mKate2_Pos
- GSM7796138 AIRE WT, input ctrl
- GSM7796139 AIRE WT, ChIP, rep1 AIRE WT, ChIP,
- GSM7796140 AIRE WT, ChIP, rep2 AIRE WT, ChIP,
- GSM7796141 AIRE DCTT.R3, input ctrl
- GSM7796142 AIRE DCTT.R3, ChIP , rep1 AIRE DCTT.R3, ChIP ,
- GSM7796143 AIRE DCTT.R3, ChIP , rep2 AIRE DCTT.R3, ChIP ,
- GSM7796144 AIRE DCARD, input ctrl
- GSM7796145 AIRE DCARD, ChIP, rep1 AIRE DCARD, ChIP,
- GSM7796146 AIRE DCARD, ChIP, rep2 AIRE DCARD, ChIP,
- GSM7796147 AIRE DPHD1, input ctrl
- GSM7796148 AIRE DPHD1, ChIP, rep1 AIRE DPHD1, ChIP,
- GSM7796149 AIRE DPHD1, ChIP, rep2 AIRE DPHD1, ChIP,
- GSM7796150 AIRE WT, DMSO, rep1 AIRE WT, DMSO,
- GSM7796151 AIRE WT, DMSO, rep2 AIRE WT, DMSO,
- GSM7796152 AIRE WT, DMSO, rep3 AIRE WT, DMSO,
- GSM7796153 AIRE WT, dCBP1, rep1 AIRE WT, dCBP1,
- GSM7796154 AIRE WT, dCBP1, rep2 AIRE WT, dCBP1,
- GSM7796155 AIRE WT, A485, rep1 AIRE WT, A485,
- GSM7796156 AIRE WT, A485, rep2 AIRE WT, A485,
- GSM7796157 AIRE WT, A485, rep3 AIRE WT, A485,
- GSM7796158 p300, no Dox, rep1 p300, no Dox,
- GSM7796159 p300, no Dox, rep2 p300, no Dox,
- GSM7796160 H3K27ac, no Dox, rep1 H3K27ac, no Dox,
- GSM7796161 H3K27ac, no Dox, rep2 H3K27ac, no Dox,
+ 35 more — browse all 75 samples with per-sample file links →
- GSE243824 Mechanism for controlled assembly of transcriptional condensates by Aire [ChIP-seq] 46 samples shares condensates, controlled, assembly, aire
- GSE299820 Innate immune epigenomic landscape following controlled human influenza virus infection 755 samples shares controlled
- GSE313072 Selective infection and loss of PRDM1+ LN Tfh cells in uncontrolled HIV infection precludes formation of Tfh reservoirs under ART 420 samples shares controlled
- GSE301505 Mutual Antagonism Between PRC1 Condensates and SWI/SNF in Chromatin Regulation 210 samples shares condensates
- GSE268960 Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in endometriod carcinomas 151 samples shares assembly
- GSE283800 Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in endometriod carcinomas [ATAC/ChIP/RNA] 145 samples shares assembly
- GSE313156 Temporal modulation of gene expression in a controlled Schistosoma mansoni human infection model 144 samples shares controlled
- GSE317503 Reference-guided genome assembly of long non-coding RNA transcripts reveals target genes associated with Crohn’s disease 140 samples shares assembly
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.