GEO series

Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells [CRISPRi]

GSE261330 Homo sapiens (human) Other 28 samples Submitted 2024/03/24 Platform GPL18573

At a glance

human · 28 samples

Organism: Homo sapiens (human)
Samples: 28 samples: 28 samples, each with a distinct title — no replicated groupsGroups 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.
Paper: Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cellsNature genetics · 2024

Summary (written by the submitters)

Cis-regulatory elements (CRE) interact with trans regulators to orchestrate gene expression, but how transcriptional regulation is coordinated in multi-gene loci has not been experimentally defined. We sought to characterize the CREs controlling dynamic expression of adjacent T cell costimulatory genes CD28, CTLA4, and ICOS encoding regulators of cell-mediated immunity.

Read the full summary ↓

Tiling CRISPR interference (CRISPRi) screens in primary human T cells – both Conventional and Regulatory subsets – uncovered gene-, cell subset- and stimulation-specific CREs. Integrating these data with CRISPR knockout (KO) screens and ATAC-seq characterization identified trans regulators influencing chromatin states at specific CRISPRi-responsive elements to control costimulatory gene expression. Lastly, we discovered and extensively validated a critical CTCF boundary that governs this locus, serving to reinforce CRE interaction with CTLA4 while also preventing promiscuous activation of CD28. By systematically mapping CREs and associated trans regulators directly in primary human T cell subsets, this work overcomes longstanding experimental limitations to decode context-dependent gene regulatory programs in a complex, multi-gene locus critical to immune homeostasis.

Published in

Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells

Mowery CT, Freimer JW, Chen Z et al. · Nature genetics 2024 · PMID 38811842 · doi:10.1038/s41588-024-01743-5

This dataset

Open GSE261330 in finder → Find more human datasets →

Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE261330_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA1086507. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38811842) ↗

Study design

28 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 28 sample titles: 28 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.

Samples in this study

GSM8140625 Donor 1 Treg, Resting, CTLA4-High
GSM8140626 Donor 1 Treg, Resting, CTLA4-Low
GSM8140627 Donor 1 Treg, 6 hour Restimulation, CTLA4-High
GSM8140628 Donor 1 Treg, 6 hour Restimulation, CTLA4-Low
GSM8140629 Donor 2 Treg, Resting, CTLA4-High
GSM8140630 Donor 2 Treg, Resting, CTLA4-Low
GSM8140631 Donor 2 Treg, 6 hour Restimulation, CTLA4-High
GSM8140632 Donor 2 Treg, 6 hour Restimulation, CTLA4-Low
GSM8140633 Donor 1 Treg, Resting, CD28-Low
GSM8140634 Donor 1 Treg, Resting, CD28-High
GSM8140635 Donor 2 Treg, Resting, CD28-Low
GSM8140636 Donor 2 Treg, Resting, CD28-High
GSM8140637 Donor 1 Treg, 24 hour Restimulation, ICOS-Low
GSM8140638 Donor 1 Treg, 24 hour Restimulation, CD28-High
GSM8140639 Donor 2 Treg, 24 hour Restimulation, ICOS-Low
GSM8140640 Donor 2 Treg, 24 hour Restimulation, CD28-High
GSM8140641 Donor 1 Tconv, Resting, CD28-High
GSM8140642 Donor 1 Tconv, Resting, CD28-Low
GSM8140643 Donor 1 Tconv, 6 hour Restimulation, CTLA4-High
GSM8140644 Donor 1 Tconv, 6 hour Restimulation, CTLA4-Low
GSM8140645 Donor 1 Tconv, 24 hour Restimulation, ICOS-High
GSM8140646 Donor 1 Tconv, 24 hour Restimulation, ICOS-Low
GSM8140647 Donor 2 Tconv, Resting, CD28-High
GSM8140648 Donor 2 Tconv, Resting, CD28-Low
GSM8140649 Donor 2 Tconv, 6 hour Restimulation, CTLA4-High
GSM8140650 Donor 2 Tconv, 6 hour Restimulation, CTLA4-Low
GSM8140651 Donor 2 Tconv, 24 hour Restimulation, ICOS-High
GSM8140652 Donor 2 Tconv, 24 hour Restimulation, ICOS-Low

Datasets on a similar topic

GSE261331 Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells [Transko] 8 samples shares context-dependent, costimulatory, systematic, multi-gene, decoding, receptor, defines, control
GSE261328 Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells [4C-seq] 4 samples shares context-dependent, costimulatory, systematic, multi-gene, decoding, receptor, defines, control
GSE261332 Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells 44 samples shares context-dependent, costimulatory, systematic, multi-gene, decoding, receptor, defines, control
GSE261329 Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells [ATAC-seq] 4 samples shares context-dependent, costimulatory, systematic, multi-gene, decoding, receptor, defines, control
GSE309650 Context-dependent effect of glucocorticoid receptor activity shapes ovarian cancer cell plasticity and therapy response 12 samples shares context-dependent, receptor
GSE305128 PreciCE: Precision engineering of cell fates via data-driven multi-gene control of transcriptional networks 3 samples shares multi-gene, control
GSE279285 Systematic characterization of the composition and dynamics of processing body-associated mRNAs 597 samples shares systematic
GSE279168 Systematic characterization of the composition and dynamics of processing body-associated mRNAs [dataset 1] 458 samples shares systematic

Search all human datasets in GEO →

Share this dataset

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.