Rapid CRISPR/Cas12a-based dual-crRNA library screening in high fidelity reveals novel genetic interactions during hepatocarcinogenesis
RNA-seq (gene expression) · mouse · 62 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 62 samples: 14 conditions, mostly in triplicateGroups 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
- High-fidelity CRISPR/Cas12a dual-crRNA screening reveals novel synergistic interactions in hepatocellular carcinomaClinical and translational medicine · 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 GSE236831_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA992483 and SRA study SRP448018. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 12 samples read as cases, 3 as controls.
How we read this: 14 replicated groups read from 62 sample titles; they account for 54 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.
- GSM7577737 SOCA library
- GSM7577738 Parallel library
- GSM7577739 Tumor_D10_rep1 Tumor_D10
- GSM7577740 Tumor_D10_rep2 Tumor_D10
- GSM7577741 Tumor_D10_rep3 Tumor_D10
- GSM7577742 Tumor_D10_rep4 Tumor_D10
- GSM7577743 Tumor_D10_rep5 Tumor_D10
- GSM7577744 Tumor_D10_rep6 Tumor_D10
- GSM7577745 Tumor_D18_rep1 Tumor_D18
- GSM7577746 Tumor_D18_rep2 Tumor_D18
- GSM7577747 Tumor_D18_rep3 Tumor_D18
- GSM7577748 Tumor_D18_rep4 Tumor_D18
- GSM7577749 Tumor_D18_rep5 Tumor_D18
- GSM7577750 Tumor_D18_rep6 Tumor_D18
- GSM7577751 Ce cell_SOCA_Day4_rep1 Ce cell_SOCA_Day4
- GSM7577752 Ce cell_SOCA_Day4_rep2 Ce cell_SOCA_Day4
- GSM7577753 Ce cell_SOCA_Day4_rep3 Ce cell_SOCA_Day4
- GSM7577754 Ce cell_SOCA_Day6_rep1 Ce cell_SOCA_Day6
- GSM7577755 Ce cell_SOCA_Day6_rep2 Ce cell_SOCA_Day6
- GSM7577756 Ce cell_SOCA_Day6_rep3 Ce cell_SOCA_Day6
- GSM7577757 Ce cell_SOCA_Day8_rep1 Ce cell_SOCA_Day8
- GSM7577758 Ce cell_SOCA_Day8_rep2 Ce cell_SOCA_Day8
- GSM7577759 Ce cell_SOCA_Day8_rep3 Ce cell_SOCA_Day8
- GSM7577760 Ce cell_SOCA_Day10_rep1 Ce cell_SOCA_Day10
- GSM7577761 Ce cell_SOCA_Day10_rep2 Ce cell_SOCA_Day10
- GSM7577762 Ce cell_SOCA_Day10_rep3 Ce cell_SOCA_Day10
- GSM7577763 Ce cell_SOCA_Day12_rep1 Ce cell_SOCA_Day12
- GSM7577764 Ce cell_SOCA_Day12_rep2 Ce cell_SOCA_Day12
- GSM7577765 Ce cell_SOCA_Day12_rep3 Ce cell_SOCA_Day12
- GSM7577766 Ce cell_SOCA_Day14_rep1 Ce cell_SOCA_Day14
- GSM7577767 Ce cell_SOCA_Day14_rep2 Ce cell_SOCA_Day14
- GSM7577768 Ce cell_SOCA_Day14_rep3 Ce cell_SOCA_Day14
- GSM7577769 Ce cell_Parallel_Day4 Ce cell_Parallel_Day
- GSM7577770 Ce cell_Parallel_Day6 Ce cell_Parallel_Day
- GSM7577771 Ce cell_Parallel_Day8 Ce cell_Parallel_Day
- GSM7577772 Ce cell_Parallel_Day10 Ce cell_Parallel_Day
- GSM7577773 Ce cell_Parallel_Day12 Ce cell_Parallel_Day
- GSM7577774 Ce cell_Parallel_Day14 Ce cell_Parallel_Day
- GSM7577775 Lb2 cell_SOCA_Day4 Lb2 cell_SOCA_Day
- GSM7577776 Lb2 cell_SOCA_Day6 Lb2 cell_SOCA_Day
+ 22 more — browse all 62 samples with per-sample file links →
- GSE255517 Rational design of immune gene therapy combinations via in vivo CRISPR activation screening of tumor microenvironment modulators 57 samples shares crispr, screening
- GSE267740 Targeting T cell plasticity by pooled single cell CRISPR-screening in preclinical models of kidney and gut inflammation 56 samples shares crispr, screening
- GSE261742 Identification of epigenetic regulators of fibrotic transformation in cardiac fibroblasts through bulk and single-cell CRISPR screens 69 samples shares crispr
- GSE306957 Mitochondrial RNA cytosolic leakage drives the SASP [CRISPR/Cas9] 34 samples shares crispr
- GSE266329 Co-culture CRISPR screens reveal ATG9A as a regulator to macrophage-mediated cytotoxicity in cancer 8 samples shares crispr
- GSE307112 Mapping the Dialogue: Decoding Alveolar Stem-Niche Interactions [I] 886 samples shares interactions
- GSE293919 Longitudinal monitoring of cytoplasmic RBP-RNA interactions and transcriptome in living cells by engineered protein nanocages 424 samples shares interactions
- GSE278418 Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues 278 samples shares interactions
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.