Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens in a dual fluorescence readthrough reporter (2)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 12 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
- 12 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
- Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporterNucleic acids research · 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 GSE243456_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 PRJNA1018532 and SRA study SRP461482. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 2 samples read as cases, 2 as controls.
How we read this: 6 replicated groups read from 12 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.
- GSM7787420 ChIP-seq of Scramble knockout, replicate 1 ChIP-seq of Scramble kn…
- GSM7787421 ChIP-seq of Scramble knockout, replicate 2 ChIP-seq of Scramble kn…
- GSM7787422 ChIP-seq of RPRD1B knockout, replicate 1 ChIP-seq of RPRD1B knoc…
- GSM7787423 ChIP-seq of RPRD1B knockout, replicate 2 ChIP-seq of RPRD1B knoc…
- GSM7787424 Scramble input ChIP, replicate 1 Scramble input ChIP,
- GSM7787425 Scramble input ChIP, replicate 2 Scramble input ChIP,
- GSM7787426 ChIP-seq of GFP, replicate 1 ChIP-seq of GFP,
- GSM7787427 ChIP-seq of GFP, replicate 2 ChIP-seq of GFP,
- GSM7787428 ChIP-seq of GFP-RPRD1B, replicate 1 ChIP-seq of GFP-RPRD1B,
- GSM7787429 ChIP-seq of GFP-RPRD1B, replicate 2 ChIP-seq of GFP-RPRD1B,
- GSM7787430 GFP input ChIP, replicate1 GFP input ChIP,
- GSM7787431 GFP input ChIP, replicate2 GFP input ChIP,
- GSE243457 Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens in a dual fluorescence readthrough reporter 28 samples shares crispr, polyadenylation, fluorescence, identifying, genome-wide, readthrough, pre-mrna, cleavage
- GSE271359 Identifying modulators of inflammation in an in vitro airway epithelial inflammation model using an arrayed CRISPRi screen 186 samples shares crispr, identifying
- GSE279036 Genome-wide CRISPR screen identifies Menin and SUZ12 as regulators of human developmental timing. 102 samples shares crispr, genome-wide
- GSE299089 A genome-wide CRISPR screen identifies the TNRC18 gene locus as a novel regulator of inflammatory signaling 54 samples shares crispr, genome-wide
- GSE330227 In vivo genome-wide CRISPR screens in human T cells to enhance T cell therapy for solid tumors 30 samples shares crispr, genome-wide
- GSE301632 Genome-wide CRISPR-Cas9 knockout screening identifies NUDCD2 depletion as sensitizer for bortezomib, carfilzomib and ixazomib in multiple myeloma. 27 samples shares crispr, genome-wide
- GSE303100 Dissecting Resistance to CDK4/6 Inhibition in Experimental Glioma via Genome-wide CRISPR-Cas9 Screening 24 samples shares crispr, genome-wide
- GSE292753 Analysis of chromatin occupancy in erythroid cells by CUT&RUN following CRISPR editing of BCL11A enhancer 33 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.