CRISPR screening reveals that RNA helicase DDX41 triggers ribosome biogenesis and cancer progression through R-loop-mediated RPL/RPS transcription
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 25 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
- 25 samples: 16 distinct titles, 3 of them repeatedGroups 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
- CRISPR screening reveals that RNA helicase DDX41 triggers ribosome biogenesis and cancer progression through R-loop-mediated RPL/RPS transcriptionNature communications · 2025
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 GSE282326_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 PRJNA1188132 and SRA study SRP546224. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 25 sample titles: 16 distinct titles with little repetition. 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.
- GSM8641399 HUH7_NC
- GSM8641401 HUH7_siDDX41-1
- GSM8641403 HUH7_siDDX41-2
- GSM8641404 HUH7_Input_DDX41_ChIP
- GSM8641405 HUH7_DDX41_ChIP
- GSM8641406 HUH7_Input_R-ChIP
- GSM8641407 HUH7_R-ChIP
- GSM8641408 HUH7_Input_H3K9ac_ChIP
- GSM8641409 HUH7_H3K9ac_ChIP
- GSM8641410 HUH7_Input_KAT8_ChIP
- GSM8641411 HUH7_KAT8_ChIP
- GSM8641412 HUH7_Input_NR2C1_ChIP
- GSM8641413 HUH7_NR2C1_ChIP
- GSM8641414 HUH7_Input_NR2C2_ChIP
- GSM8641415 HUH7_NR2C2_ChIP
- GSM8641416 CRISPR_C1
- GSM8641417 CRISPR_C2
- GSM8641418 CRISPR_C3
- GSM8641419 CRISPR_C4
- GSM8641420 CRISPR_C5
- GSM8641421 CRISPR_T1
- GSM8641422 CRISPR_T2
- GSM8641423 CRISPR_T3
- GSM8641424 CRISPR_T4
- GSM8641425 CRISPR_T5
- GSE276052 CRISPR screening identifies regulators of enhancer mediated androgen receptor transcription in advanced prostate cancer 92 samples shares crispr, transcription
- GSE290213 A single cell transcriptional profile of benign prostatic hyperplasia 27 samples shares rpl, transcription
- GSE242372 FACT orchestrates the interplay between chromatin structure and transcription [ChIP-Seq] 16 samples shares rpl, transcription
- GSE275927 CRISPR screening identifies regulators of enhancer mediated androgen receptor transcription in advanced prostate cancer (ATAC-Seq) 8 samples shares crispr, transcription
- GSE245249 CRISPR activation screens identify the SWI-SNF ATPases as suppressors of ferroptosis 65 samples shares crispr
- GSE261284 Bioinformatics and single-cell CRISPRi-based screen reveals effector genes and implicates multi-tissue etiology for BMD 53 samples shares crispr
- GSE288996 Simultaneous single cell CRISPR, RNA, and ATAC-seq enables multiomic CRISPR screens to identify gene regulatory relationships 15 samples shares crispr
- GSE317890 Transcriptomic profiling of interferon responses induced by IVT sgRNAs in CRISPRi HEK293T cells 360 samples shares crispr
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.