Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens in a dual fluorescence readthrough reporter
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 28 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
- 28 samples: 10 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
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 GSE243457_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 PRJNA1018528 and SRA study SRP458857. 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: 10 replicated groups read from 28 sample titles; they account for 28 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.
- GSM7764458 CPEB2.PAS.Unsorted. replicate 1 CPEB2.PAS.Unsorted
- GSM7764459 CPEB2.PAS.Unsorted. replicate 2 CPEB2.PAS.Unsorted
- GSM7764460 CPEB2.PAS.Unsorted. replicate 3 CPEB2.PAS.Unsorted
- GSM7764461 CPEB2.PAS.Unsorted. replicate 4 CPEB2.PAS.Unsorted
- GSM7764462 CPEB2.PAS.Sorted.replicate 1 CPEB2.PAS.Sorted
- GSM7764463 CPEB2.PAS.Sorted.replicate 2 CPEB2.PAS.Sorted
- GSM7764464 CPEB2.PAS.Sorted.replicate 3 CPEB2.PAS.Sorted
- GSM7764465 CPEB2.PAS.Sorted.replicate 4 CPEB2.PAS.Sorted
- GSM7764466 CCND2.PAS.Unsorted.replicate 1 CCND2.PAS.Unsorted
- GSM7764467 CCND2.PAS.Unsorted.replicate 2 CCND2.PAS.Unsorted
- GSM7764468 CCND2.PAS.Unsorted.replicate 3 CCND2.PAS.Unsorted
- GSM7764469 CCND2.PAS.Unsorted.replicate 4 CCND2.PAS.Unsorted
- GSM7764470 CCND2.PAS.Sorted.replicate 1 CCND2.PAS.Sorted
- GSM7764471 CCND2.PAS.Sorted.replicate 2 CCND2.PAS.Sorted
- GSM7764472 CCND2.PAS.Sorted.replicate 3 CCND2.PAS.Sorted
- GSM7764473 CCND2.PAS.Sorted.replicate 4 CCND2.PAS.Sorted
- 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,
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- GSE317890 Transcriptomic profiling of interferon responses induced by IVT sgRNAs in CRISPRi HEK293T cells 360 samples shares crispr
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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.