Rapid CRISPR/Cas12a-based dual-crRNA library screening in high fidelity reveals novel genetic interactions during hepatocarcinogenesis [RNA-Seq]
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 3 × WT vs 3 × crRaf1 vs 3 × crPkm2 vs 3 × crRaf1_crPkm2Groups 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
Read the full summary ↓
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 GSE236826_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 PRJNA992494 and SRA study SRP448018. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM7577795 WT_rep1 WT
- GSM7577796 WT_rep2 WT
- GSM7577797 WT_rep3 WT
- GSM7577798 crRaf1_rep1 crRaf1
- GSM7577799 crRaf1_rep2 crRaf1
- GSM7577800 crRaf1_rep3 crRaf1
- GSM7577801 crPkm2_rep1 crPkm2
- GSM7577802 crPkm2_rep2 crPkm2
- GSM7577803 crPkm2_rep3 crPkm2
- GSM7577804 crRaf1_crPkm2_rep1 crRaf1_crPkm2
- GSM7577805 crRaf1_crPkm2_rep2 crRaf1_crPkm2
- GSM7577806 crRaf1_crPkm2_rep3 crRaf1_crPkm2
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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.