ARF alters PAF1 complex integrity to selectively repress oncogenic transcription programs upon p53 loss
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 14 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
- 14 samples: 6 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
- ARF alters PAF1 complex integrity to selectively repress oncogenic transcription programs upon p53 lossMolecular cell · 2024
Read the full summary ↓
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 GSE217765_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 PRJNA900287 and SRA study SRP407286. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 14 sample titles; they account for 12 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.
- GSM6725916 shNT, RPB3, rep1 shNT, RPB3,
- GSM6725917 shNT, RPB3, rep2 shNT, RPB3,
- GSM6725918 shARF, RPB3, rep1 shARF, RPB3,
- GSM6725919 shARF, RPB3, rep2 shARF, RPB3,
- GSM6725920 shNT, PAF1, rep1 shNT, PAF1,
- GSM6725921 shNT, PAF1, rep2 shNT, PAF1,
- GSM6725922 shARF, PAF1, rep1 shARF, PAF1,
- GSM6725923 shARF, PAF1, rep2 shARF, PAF1,
- GSM6725924 shNT, CTR9, rep1 shNT, CTR9,
- GSM6725925 shNT, CTR9, rep2 shNT, CTR9,
- GSM6725926 shARF, CTR9, rep1 shARF, CTR9,
- GSM6725927 shARF, CTR9, rep2 shARF, CTR9,
- GSM6725928 shNT, Input
- GSM6725929 shARF, Input
- GSE268172 Stable maintenance of MERVL-positive embryonic stem cells reveals sustained transcriptional programs and enhancer remodeling 45 samples shares transcription, programs
- GSE271884 GFI1-driven transcriptional and epigenetic programs maintain memory CD8+ T cell persistence [ATAC-seq]. 30 samples shares transcription, programs
- GSE300113 Heterogenous microglial reactivity contrasts with stable vascular transcriptional programs in mouse models of Alzheimer’s, CADASIL, and Traumatic Brain Injury (Main dataset) 59 samples shares transcription, programs
- GSE273878 Cancer-induced FOXP1 disrupts and reprograms skeletal muscle circadian transcription in cachexia [circadian RNA-seq] 48 samples shares transcription, programs
- GSE241378 Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of embryonic stem cell maintenance and neuronal differentiation. 36 samples shares transcription, programs
- GSE202694 The transcriptional factor ONECUT3 is a driver and therapeutic target for complex karyotype MDS 12 samples shares transcription, complex
- GSE283958 Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators 47 samples shares transcription
- GSE326173 Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by regulating expression of AP-1 transcription factors and their target genes [ChIP-seq] 42 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.