Paired CRISPR screens to map gene regulation in cis and trans (CUT&RUN)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 30 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
- 30 samples: 30 samples, each with a distinct title — no replicated groupsGroups 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.
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 GSE255699_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 PRJNA1076336 and SRA study SRP489622. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 30 sample titles: 30 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.
- GSM8078015 BxPC3, SRF, Replicate1, CUT&RUN
- GSM8078016 BxPC3, SRF, Replicate2, CUT&RUN
- GSM8078017 BxPC3, SRF, Replicate3, CUT&RUN
- GSM8078018 BxPC3, BPTF, Replicate1, CUT&RUN
- GSM8078019 BxPC3, BPTF, Replicate2, CUT&RUN
- GSM8078020 BxPC3, BPTF, Replicate3, CUT&RUN
- GSM8078021 BxPC3, H3K4me3, Replicate1, CUT&RUN
- GSM8078022 BxPC3, H3K4me3, Replicate2, CUT&RUN
- GSM8078023 BxPC3, H3K4me3, Replicate3, CUT&RUN
- GSM8078024 BxPC3, IgG, Replicate1, CUT&RUN
- GSM8078025 BxPC3, IgG, Replicate2, CUT&RUN
- GSM8078026 BxPC3, IgG, Replicate3, CUT&RUN
- GSM9829716 BxPC3, H3K27ac, no IFNγ, Replicate1, CUT&RUN
- GSM9829717 BxPC3, H3K27ac, no IFNγ, Replicate2, CUT&RUN
- GSM9829718 BxPC3, H3K27ac, no IFNγ, Replicate3, CUT&RUN
- GSM9829719 BxPC3, H3K4me3, no IFNγ, Replicate1, CUT&RUN
- GSM9829720 BxPC3, H3K4me3, no IFNγ, Replicate2, CUT&RUN
- GSM9829721 BxPC3, H3K4me3, no IFNγ, Replicate3, CUT&RUN
- GSM9829722 BxPC3, IgG, no IFNγ, Replicate1, CUT&RUN
- GSM9829723 BxPC3, IgG, no IFNγ, Replicate2, CUT&RUN
- GSM9829724 BxPC3, IgG, no IFNγ, Replicate3, CUT&RUN
- GSM9829725 BxPC3, H3K27ac, plus IFNγ, Replicate1, CUT&RUN
- GSM9829726 BxPC3, H3K27ac, plus IFNγ, Replicate2, CUT&RUN
- GSM9829727 BxPC3, H3K27ac, plus IFNγ, Replicate3, CUT&RUN
- GSM9829728 BxPC3, H3K4me3, plus IFNγ, Replicate1, CUT&RUN
- GSM9829729 BxPC3, H3K4me3, plus IFNγ, Replicate2, CUT&RUN
- GSM9829730 BxPC3, H3K4me3, plus IFNγ, Replicate3, CUT&RUN
- GSM9829731 BxPC3, IgG, plus IFNγ, Replicate1, CUT&RUN
- GSM9829732 BxPC3, IgG, plus IFNγ, Replicate2, CUT&RUN
- GSM9829733 BxPC3, IgG, plus IFNγ, Replicate3, CUT&RUN
- GSE278910 Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling [CUT&RUN] 30 samples shares crispr, cut, run, screens, trans
- GSE253893 PAX translocations remodel mitochondrial metabolism through altered leucine usage in rhabdomyosarcoma [Cut&Run] 28 samples shares cut, run, trans
- GSE267470 Dual targeting of processive transcription for Myc-driven circuitry in medulloblastoma [CUT&RUN] 12 samples shares cut, run, trans
- GSE270503 Epigenetic heterogeneity and state-specific transcriptional programs determine differential drug response in osteosarcoma [Cut&Run] 56 samples shares cut, run, trans
- GSE301512 Chromatin topology dynamics of dexamethasone-treated trabecular meshwork identifies 78 causal genes for intraocular pressure and primary open angle glaucoma [CUT&Run] 30 samples shares cut, run
- GSE316989 Targeting CDK12/CYCLIN K induces a gene activation program which is mediated by P-TEFb [Cut&RUN] 10 samples shares cut, run
- GSE303343 A unified network systems approach uncovers a core program underlying T follicular helper cell differentiation [CUT&RUN] 48 samples shares cut, run
- GSE287902 BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [Cut&Run] 40 samples shares cut, run
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.