Analysis of nascent transcription in ES cells mutant for specific TFIID subunits
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 55 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
- 55 samples: 21 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
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE245196_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1027343 and SRA study SRP515105. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 51 samples.
How we read this: 21 replicated groups read from 55 sample titles; they account for 51 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.
- 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
- GSM7838573 RT7_vehicle_rep1 RT7_vehicle
- GSM7838574 RT7_vehicle_rep2 RT7_vehicle
- GSM7838575 RT7_vehicle_rep3 RT7_vehicle
- GSM7838576 RT7 _4OHT_rep1 RT7 _4OHT
+ 15 more — browse all 55 samples with per-sample file links →
- GSE288261 A Novel Microglia-Specific Transcriptional Signatures Correlates with Behavioural Deficits in Neuropsychiatric Lupus (NP-SLE) 28 samples shares transcription, specific
- GSE283392 Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function 25 samples shares transcription, specific
- GSE305064 FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry [mouse_Tconv_ChIP-seq] 15 samples shares transcription, specific
- GSE348719 Longitudinal Machine Learning and snRNA-Seq Reveal Stroke-Specific Behavioral and Transcriptional Signatures 10 samples shares transcription, specific
- GSE229592 Transcription factor Ikzf1 associates with Foxp3 to repress gene expression in Treg cells and limit autoimmunity and anti-tumor immunity 32 samples shares transcription
- GSE283483 Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression programs in the hippocampus 160 samples shares specific
- GSE282097 Diminished transcriptional activity and splicing changes drive gene length-biased rewiring in the aging transcriptome 116 samples shares transcription
- GSE282280 DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation. 93 samples shares transcription
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.