GEO series

Analysis of nascent transcription in ES cells mutant for specific TFIID subunits [CUT&Run]

GSE245194 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 36 samples Submitted 2024/10/01 Platform GPL30172

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 36 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: Mus musculus (mouse)
Samples: 36 samples: 16 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: RNA polymerase II transcription initiation in holo-TFIID-depleted mouse embryonic stem cellsCell reports · 2024

Summary (written by the submitters)

RNA polymerase II (Pol II) transcription initiation starts with the assembly of the preinitiation complex (PIC) on core promoters. The PIC is composed of six general transcription factors (GTFs). The recognition of the core promoter sequences by the TFIID GTF complex is the first step of the PIC assembly. In metazoans, holo-TFIID is composed of the TATA binding protein (TBP) and of 13 TBP associated factors (TAFs).

Read the full summary ↓

Genetic depletion of different murine TAFs have shown that TAFs such as TAF7 or TAF10, can be either required, or dispensable for Pol II transcription, depending on different cellular contexts. In this report, we depleted TAF7 and/or TAF10 in the same cellular system; either in mesodermal progenitors during mouse development or in mESCs. In these two models, TAF7 depletion leads to a milder phenotype compared to TAF10 depletion. As TAF10 is also a subunit of the transcriptional co-activator Spt-Ada-Gcn5 acetyl transferase (SAGA), we first showed that the difference in phenotype between the Taf7 and Taf10 mutant is not due to the SAGA effect, at least for mESCs. Immunoprecipitations coupled with mass spectrometry analyses from mESCs lysates assembly of holo-TFIID complex is rapidly affected after induction of the depletion. In line with the model of holo-TFIID sequential assembly, TAF10 depletion leads to an early defect with formation of the core-TFIID, while TAF7 depletion results in the formation of a TAF7-less TFIID. Thus, the difference in phenotype severity correlates with the degree of TFIID disassembly. Surprisingly, no major global changes in Pol II transcription could be observed after either TAF7 or TAF10 depletion. Our data suggest that the inducible loss of fully assembled canonical TFIID does not correlate with the lack of global Pol II transcription activity changes suggesting that partially assembled TFIID complexes can participate in Pol II transcription initiation, with only limited effect on Pol II nascent transcription.

Published in

RNA polymerase II transcription initiation in holo-TFIID-depleted mouse embryonic stem cells

Hisler V, Bardot P, Detilleux D et al. · Cell reports 2024 · PMID 39352809 · doi:10.1016/j.celrep.2024.114791

This dataset

Open GSE245194 in finder → Find more mouse 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 GSE245194_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 PRJNA1027351 and SRA study SRP466069. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39352809) ↗

Study design

16 conditions, mostly in duplicate

RT7 EtOH TBP ×2 RT7 4-OHT TBP ×2 RT10 EtOH TBP ×2 RT10 4-OHT TBP ×2 RT7 EtOH TAF7 ×2 RT7 4-OHT TAF7 ×2 RT10 EtOH TAF7 ×2 RT10 4-OHT TAF7 ×2 +12 more

Supports a between-group comparison across 32 samples.

How we read this: 16 replicated groups read from 36 sample titles; they account for 32 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

GSM7838537 RT7 EtOH TBP rep1 RT7 EtOH TBP
GSM7838538 RT7 EtOH TBP rep2 RT7 EtOH TBP
GSM7838539 RT7 4-OHT TBP rep1 RT7 4-OHT TBP
GSM7838540 RT7 4-OHT TBP rep2 RT7 4-OHT TBP
GSM7838541 RT10 EtOH TBP rep1 RT10 EtOH TBP
GSM7838542 RT10 EtOH TBP rep2 RT10 EtOH TBP
GSM7838543 RT10 4-OHT TBP rep1 RT10 4-OHT TBP
GSM7838544 RT10 4-OHT TBP rep2 RT10 4-OHT TBP
GSM7838545 RT7 EtOH TAF7 rep1 RT7 EtOH TAF7
GSM7838546 RT7 EtOH TAF7 rep2 RT7 EtOH TAF7
GSM7838547 RT7 4-OHT TAF7 rep1 RT7 4-OHT TAF7
GSM7838548 RT7 4-OHT TAF7 rep2 RT7 4-OHT TAF7
GSM7838549 RT10 EtOH TAF7 rep1 RT10 EtOH TAF7
GSM7838550 RT10 EtOH TAF7 rep2 RT10 EtOH TAF7
GSM7838551 RT10 4-OHT TAF7 rep1 RT10 4-OHT TAF7
GSM7838552 RT10 4-OHT TAF7 rep2 RT10 4-OHT TAF7
GSM7838553 RT7 EtOH TAF10 rep1 RT7 EtOH TAF10
GSM7838554 RT7 EtOH TAF10 rep2 RT7 EtOH TAF10
GSM7838555 RT7 4-OHT TAF10 rep1 RT7 4-OHT TAF10
GSM7838556 RT7 4-OHT TAF10 rep2 RT7 4-OHT TAF10
GSM7838557 RT10 EtOH TAF10 rep1 RT10 EtOH TAF10
GSM7838558 RT10 EtOH TAF10 rep2 RT10 EtOH TAF10
GSM7838559 RT10 4-OHT TAF10 rep1 RT10 4-OHT TAF10
GSM7838560 RT10 4-OHT TAF10 rep2 RT10 4-OHT TAF10
GSM7838561 RT7 EtOH TAF12 rep1 RT7 EtOH TAF12
GSM7838562 RT7 EtOH TAF12 rep2 RT7 EtOH TAF12
GSM7838563 RT7 4-OHT TAF12 rep1 RT7 4-OHT TAF12
GSM7838564 RT7 4-OHT TAF12 rep2 RT7 4-OHT TAF12
GSM7838565 RT10 EtOH TAF12 rep1 RT10 EtOH TAF12
GSM7838566 RT10 EtOH TAF12 rep2 RT10 EtOH TAF12
GSM7838567 RT10 4-OHT TAF12 rep1 RT10 4-OHT TAF12
GSM7838568 RT10 4-OHT TAF12 rep2 RT10 4-OHT TAF12
GSM7838569 RT7 EtOH IgG
GSM7838570 RT7 4-OHT IgG
GSM7838571 RT10 EtOH IgG
GSM7838572 RT10 4-OHT IgG

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