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Manipulating the transcriptome and chromatin accessibility in T cells through CRISPR-induced alternative splicing of IKZF1 (ATACseq)

GSE255337 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 34 samples Submitted 2024/06/01 Platform GPL21697
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 34 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
34 samples: 8 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
Manipulation of Alternative Splicing of IKZF1 Elicits Distinct Gene Regulatory Responses in T CellsCells · 2026
Summary (written by the submitters)
Genome-wide association studies have identified statistically significant associations between genetic variants in or near the IKZF1 gene and several autoimmune disorders. IKZF1, encoding the transcription factor Ikaros, produces at least 10 distinct transcripts via alternative splicing. To explore the role of alternative splicing of IKZF1 in mature T cells, we generated a panel of Jurkat T-cell clones with various truncating mutations in IKZF1 exon 4, exon 6 or both.
Read the full summary ↓
Differences among clones in gene expression, chromatin accessibility, and protein abundance were assessed by RNA-seq, ATAC-seq and immunoblotting. Clones with single targeting events in either exon 4 or 6 clustered separately from double-targeted clones on multiple parameters, but overall, clone responses were highly heterogeneous. Perturbation of IKZF1 splicing resulted in significant differences in expression and chromatin accessibility of other autoimmunity-associated genes and elicited compensatory expression changes in other IKZF family members. Our results suggest that even modest perturbations of IKZF1 splicing can have significant effects on gene expression and function in mature T cells.
Published in
Manipulation of Alternative Splicing of IKZF1 Elicits Distinct Gene Regulatory Responses in T Cells
Pastor L, Newman JRB, Callahan CM et al. · Cells 2026 · PMID 41677588 · doi:10.3390/cells15030221
This dataset
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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 GSE255337_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 PRJNA1074710 and SRA study SRP488951. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41677588) ↗
Study design
8 conditions, mostly in triplicate
ATAC_IKZF1-Ex5-Ex3-sg1-C ×9 ATAC_IKZF1-Ex3-sg1-C ×6 ATAC_SIRPG-Ex4-sg1-C ×5 ATAC_IKZF1-Ex5-sg1-C ×3 ATAC_IKZF1-Ex5-sg2-C ×3 ATAC_IKZF4-Ex2-sg1-C ×3 ATAC_IKZF4-Ex3-sg1-C ×3 ATAC_IKZF1-Ex3-sg2-C ×2

Supports a between-group comparison across 34 samples.

How we read this: 8 replicated groups read from 34 sample titles; they account for 34 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
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