RNA-DNA hybrids formed in the absence of Senataxin drive non-coding RNA expression and protein aggregation in the nucleolus
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 17 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
- 17 samples: 5 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
- Senataxin deficiency disrupts proteostasis through nucleolar ncRNA-driven protein aggregationThe Journal of cell biology · 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 GSE240664_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 PRJNA1004589 and SRA study SRP454675. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 13 samples.
How we read this: 5 replicated groups read from 17 sample titles; they account for 13 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.
- GSM7707213 R-ChIP control rep1 R-ChIP control
- GSM7707214 R-ChIP control rep2 R-ChIP control
- GSM7707215 R-ChIP SETX KO rep1 R-ChIP SETX KO
- GSM7707216 R-ChIP SETX KO rep2 R-ChIP SETX KO
- GSM7707217 control rep1 input
- GSM7707218 control rep2 input
- GSM7707219 SETX KO rep1 input
- GSM7707220 SETX KO rep2 input
- GSM7707221 TGIRT RNAseq control rep1 TGIRT RNAseq control
- GSM7707222 TGIRT RNAseq control rep2 TGIRT RNAseq control
- GSM7707223 TGIRT RNAseq control rep3 TGIRT RNAseq control
- GSM7707224 TGIRT RNAseq shSETX rep1 TGIRT RNAseq shSETX
- GSM7707225 TGIRT RNAseq shSETX rep2 TGIRT RNAseq shSETX
- GSM7707226 TGIRT RNAseq shSETX rep3 TGIRT RNAseq shSETX
- GSM7707227 TGIRT RNAseq SETX KO rep1 TGIRT RNAseq SETX KO
- GSM7707228 TGIRT RNAseq SETX KO rep2 TGIRT RNAseq SETX KO
- GSM7707229 TGIRT RNAseq SETX KO rep3 TGIRT RNAseq SETX KO
- GSE233479 Regulation of transcription patterns, poly(ADP-ribose), and RNA-DNA hybrids by the ATM protein kinase 52 samples shares rna-dna, hybrids, protein
- GSE254536 Replication Fork-Associated RNA-DNA Hybrids Safeguard Genomic Stability in Transcriptionally Active Regions 87 samples shares rna-dna, hybrids
- GSE254534 Replication Fork-Associated RNA-DNA Hybrids Safeguard Genomic Stability in Transcriptionally Active Regions [DNA2_MRE11_ChIPseq] 9 samples shares rna-dna, hybrids
- GSE303136 DEAD-Box Helicase 3 Modulates the Non-Coding RNA Pool in Ribonucleoprotein Condensates During Stress Granule Formation 24 samples shares non-coding, protein
- GSE197454 NGLY1 mutations cause protein aggregation in human neurons 16 samples shares aggregation, protein
- GSE139626 Mutual repression of the RNA-binding protein PCBP2 and long non-coding RNAs in induced pluripotent stem cells 10 samples shares non-coding, protein
- GSE252173 Dynamic Control of RNA-DNA Hybrid Formation Orchestrates DNA2 Activation at Stalled Forks by RNAPII and DDX39A. 42 samples shares rna-dna
- GSE252171 Dynamic Control of RNA-DNA Hybrid Formation Orchestrates DNA2 Activation at Stalled Forks by RNAPII and DDX39A [RNA-seq] 36 samples shares rna-dna
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.