Genome-wide CRISPR screening identifies the E3 ubiquitin ligase HERC1 as a modulator of the response to nucleoside analogs in acute myeloid leukemia
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 × sgCtrl-drug_6h vs 3 × sgCtrl-vehicle vs 3 × sgHerc1_Clone-E5-drug_6h vs 3 × sgHerc1_Clone-E5-vehicleGroups 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
- The E3 ubiquitin ligase Herc1 modulates the response to nucleoside analogs in acute myeloid leukemiaBlood advances · 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 GSE273667_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 PRJNA1142585 and SRA study SRP523405. 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.
- GSM8434905 sgCtrl-drug_6h-1 sgCtrl-drug_6h
- GSM8434906 sgCtrl-drug_6h-2 sgCtrl-drug_6h
- GSM8434907 sgCtrl-drug_6h-3 sgCtrl-drug_6h
- GSM8434908 sgCtrl-vehicle-1 sgCtrl-vehicle
- GSM8434909 sgCtrl-vehicle-2 sgCtrl-vehicle
- GSM8434910 sgCtrl-vehicle-3 sgCtrl-vehicle
- GSM8434911 sgHerc1_Clone-E5-drug_6h-1 sgHerc1_Clone-E5-drug_6h
- GSM8434912 sgHerc1_Clone-E5-drug_6h-2 sgHerc1_Clone-E5-drug_6h
- GSM8434913 sgHerc1_Clone-E5-drug_6h-3 sgHerc1_Clone-E5-drug_6h
- GSM8434914 sgHerc1_Clone-E5-vehicle-1 sgHerc1_Clone-E5-vehicle
- GSM8434915 sgHerc1_Clone-E5-vehicle-2 sgHerc1_Clone-E5-vehicle
- GSM8434916 sgHerc1_Clone-E5-vehicle-3 sgHerc1_Clone-E5-vehicle
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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.