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Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [RNA-seq]

GSE234248 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2024/03/11 Platform GPL17021Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 24 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
24 samples: 11 conditions, mostly in duplicateGroups 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
Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCFNature genetics · 2024
Summary (written by the submitters)
Catalytic activity of the ISWI family of remodelers is critical for nucleosomal organization and transcription factor binding, including the insulator protein CTCF. To define which subcomplex mediate these diverse functions we phenotyped a panel of isogenic mouse stem cell lines each lacking one of six ISWI accessory subunits.
Read the full summary ↓
Individual deletions of either CERF, RSF1, ACF, WICH or NoRC subcomplexes cause only moderate effects on the chromatin landscape, while removal of the NURF specific subunit BPTF leads to drastic reduction in chromatin accessibility and Snf2h ATPase localization around CTCF sites. While this reduces distances to the adjacent nucleosomes it only modestly impacts CTCF binding itself. In absence of accessibility bound CTCF is nevertheless impaired in function resulting in lower occupancy of cohesin and cohesin-loading factors, and reduced insulation at these sites, highlighting the need of NURF-mediated remodeling for open chromatin and proper CTCF function. Our comprehensive analysis reveals a specific role for NURF in mediating Snf2h localization and chromatin opening at bound CTCF sites showing that local accessibility is critical for cohesin binding and insulator function.
Published in
Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF
Iurlaro M, Masoni F, Flyamer IM et al. · Nature genetics 2024 · PMID 38816647 · doi:10.1038/s41588-024-01767-x
This dataset
Open GSE234248 in finder → Find more mouse RNA-seq 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 GSE234248_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA980622 and SRA study SRP441350. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38816647) ↗
Study design
11 conditions, mostly in duplicate
RNAseq_ESC_wt_D ×3 RNAseq_ESC_cecr_ko_D ×3 RNAseq_ESC_wt_A ×2 RNAseq_ESC_rsf1_ko_A ×2 RNAseq_ESC_wstf_ko_A ×2 RNAseq_ESC_wt_B ×2 RNAseq_ESC_tip5_ko_B ×2 RNAseq_ESC_wt_C ×2 +3 more

Supports a between-group comparison across 24 samples.

How we read this: 11 replicated groups read from 24 sample titles; they account for 24 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
Datasets on a similar topic

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