Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq
Single-cell RNA-seq · mouse · 70 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Mus musculus (mouse)
- Samples
- 70 samples
- 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 GSE90488_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 PRJNA354864 and SRA study SRP093880. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 70 more — browse all 70 samples with per-sample file links →
- GSE334845 Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors [RNA-Seq] 86 samples shares crispr, screens, rna-seq
- GSE261783 Identification of epigenetic regulators of fibrotic transformation in cardiac fibroblasts through bulk and single-cell CRISPR screens [scRNA-seq] 10 samples shares crispr, screens, rna-seq
- GSE263759 Integrated time-series analysis and high-content CRISPR screening delineate the dynamics of macrophage immune regulation [RNA-seq] 64 samples shares crispr, rna-seq
- GSE334890 Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors 48 samples shares crispr, screens
- GSE269446 In vivo CRISPR screens in Head and Neck Cancer reveal that Uchl5 modulates extracellular matrix deposition to promote immune evasion 23 samples shares crispr, screens
- GSE255514 Rational design of immune gene therapy combinations via in vivo CRISPR activation screening of tumor microenvironment modulators [Bulk RNA-seq] 15 samples shares crispr, rna-seq
- GSE338899 In vivo CRISPR screens identify dual functions of DNMT3A in mediating tumor immune evasion 12 samples shares crispr, screens
- GSE269444 In vivo CRISPR screens in Head and Neck Cancer reveal that Uchl5 modulates extracellular matrix deposition to promote immune evasion [in vitro] 12 samples shares crispr, screens
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.