Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling [CUT&RUN]
Single-nucleus RNA-seq · human · 30 samples
- What it is
- Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
- Organism
- Homo sapiens (human)
- Samples
- 30 samples: 6 conditions, mostly with about 5 replicates eachGroups 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
- Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profilingNature biotechnology · 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 GSE278910_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1169554 and SRA study SRP536880. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 30 samples.
How we read this: 6 replicated groups read from 30 sample titles; they account for 30 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.
- GSM8557337 NT_H2AZ_1 NT_H2AZ
- GSM8557338 NT_H2AZ_2 NT_H2AZ
- GSM8557339 NT_H2AZ_3 NT_H2AZ
- GSM8557340 NT_H2AZ_4 NT_H2AZ
- GSM8557341 NT_H2AZ_5 NT_H2AZ
- GSM8557342 NT_H3K4me3_1 NT_H3K4me3
- GSM8557343 NT_H3K4me3_2 NT_H3K4me3
- GSM8557344 NT_H3K4me3_3 NT_H3K4me3
- GSM8557345 NT_H3K4me3_4 NT_H3K4me3
- GSM8557346 NT_H3K4me3_5 NT_H3K4me3
- GSM8557347 NT_IgG_1 NT_IgG
- GSM8557348 NT_IgG_2 NT_IgG
- GSM8557349 NT_IgG_3 NT_IgG
- GSM8557350 NT_IgG_4 NT_IgG
- GSM8557351 NT_IgG_5 NT_IgG
- GSM8557352 ZNHIT1_H2AZ_1 ZNHIT1_H2AZ
- GSM8557353 ZNHIT1_H2AZ_2 ZNHIT1_H2AZ
- GSM8557354 ZNHIT1_H2AZ_3 ZNHIT1_H2AZ
- GSM8557355 ZNHIT1_H2AZ_4 ZNHIT1_H2AZ
- GSM8557356 ZNHIT1_H2AZ_5 ZNHIT1_H2AZ
- GSM8557357 ZNHIT1_H3K4me3_1 ZNHIT1_H3K4me3
- GSM8557358 ZNHIT1_H3K4me3_2 ZNHIT1_H3K4me3
- GSM8557359 ZNHIT1_H3K4me3_3 ZNHIT1_H3K4me3
- GSM8557360 ZNHIT1_H3K4me3_4 ZNHIT1_H3K4me3
- GSM8557361 ZNHIT1_H3K4me3_5 ZNHIT1_H3K4me3
- GSM8557362 ZNHIT1_IgG_1 ZNHIT1_IgG
- GSM8557363 ZNHIT1_IgG_2 ZNHIT1_IgG
- GSM8557364 ZNHIT1_IgG_3 ZNHIT1_IgG
- GSM8557365 ZNHIT1_IgG_4 ZNHIT1_IgG
- GSM8557366 ZNHIT1_IgG_5 ZNHIT1_IgG
- GSE287902 BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [Cut&Run] 40 samples shares cut, run, accessibility, chromatin
- 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, chromatin
- GSE308629 Pooled CRISPR screens identify genes and non-coding genomic regions that regulate red blood cell density 99 samples shares crispr, screens, pooled
- GSE303343 A unified network systems approach uncovers a core program underlying T follicular helper cell differentiation [CUT&RUN] 48 samples shares cut, run
- GSE253893 PAX translocations remodel mitochondrial metabolism through altered leucine usage in rhabdomyosarcoma [Cut&Run] 28 samples shares cut, run
- GSE267470 Dual targeting of processive transcription for Myc-driven circuitry in medulloblastoma [CUT&RUN] 12 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
- GSE270503 Epigenetic heterogeneity and state-specific transcriptional programs determine differential drug response in osteosarcoma [Cut&Run] 56 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.