Foxd1 expression identifies a distinct subset of hepatic stellate cells involved in liver fibrosis
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 × HSC vs 3 × HSC_Tom vs 3 × HSC_CCl4 vs 3 × HSC_CCl4_TomGroups 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
- FoxD1 expression identifies a distinct subset of hepatic stellate cells involved in liver fibrosisBiochemical and biophysical research communications · 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 GSE270404_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 PRJNA1126310 and SRA study SRP515116. 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.
- GSM8342012 HSC-1 HSC
- GSM8342013 HSC-2 HSC
- GSM8342014 HSC-3 HSC
- GSM8342015 HSC_Tom-1 HSC_Tom
- GSM8342016 HSC_Tom-2 HSC_Tom
- GSM8342017 HSC_Tom-3 HSC_Tom
- GSM8342018 HSC_CCl4-1 HSC_CCl4
- GSM8342019 HSC_CCl4-2 HSC_CCl4
- GSM8342020 HSC_CCl4-3 HSC_CCl4
- GSM8342021 HSC_CCl4_Tom-1 HSC_CCl4_Tom
- GSM8342022 HSC_CCl4_Tom-2 HSC_CCl4_Tom
- GSM8342023 HSC_CCl4_Tom-3 HSC_CCl4_Tom
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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.