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RORA proximal enhancer regulates its expression during early human Th17 cell differentiation

GSE243064 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 72 samples Submitted 2024/05/23 Platform GPL16791
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 72 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
72 samples: 16 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
A proximal enhancer regulates RORA expression during early human Th17 cell differentiationClinical immunology (Orlando, Fla.) · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
A proximal enhancer regulates RORA expression during early human Th17 cell differentiation
Kalim UU, Biradar R, Junttila S et al. · Clinical immunology (Orlando, Fla.) 2024 · PMID 38788884 · doi:10.1016/j.clim.2024.110261
This dataset
Open GSE243064 in finder → Find more human ChIP / ATAC / CUT&Tag datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE243064_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1016309 and SRA study SRP460179. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38788884) ↗
Study design
16 conditions, mostly in triplicate
Th0_0.5h_Input ×3 Th0_0.5h_H3K4me1 ×3 Th0_0.5h_H3K4me3 ×3 Th0_0.5h_H3K27ac ×3 Th17_0.5h_Input ×3 Th17_0.5h_H3K4me1 ×3 Th17_0.5h_H3K4me3 ×3 Th17_0.5h_H3K27ac ×3 +32 more

Supports a between-group comparison across 48 samples.

How we read this: 16 replicated groups read from 72 sample titles; they account for 48 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.

Samples in this study

+ 32 more — browse all 72 samples with per-sample file links →

Datasets on a similar topic

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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.