Identification of hepatocyte-primed biliary epithelial cells in the homeostatic liver by in vivo lentiviral gene transfer to mice and non-human primates [1]
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: 6 × EpCAM, ConfettiNeg, vs 6 × EpCAM, ConfettiPos,Groups 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.
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 GSE232369_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 PRJNA971874 and SRA study SRP437352. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 2 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.
- GSM7329518 EpCAM, ConfettiNeg, 1 EpCAM, ConfettiNeg,
- GSM7329519 EpCAM, ConfettiNeg, 2 EpCAM, ConfettiNeg,
- GSM7329520 EpCAM, ConfettiNeg, 3 EpCAM, ConfettiNeg,
- GSM7329521 EpCAM, ConfettiNeg, 4 EpCAM, ConfettiNeg,
- GSM7329522 EpCAM, ConfettiNeg, 5 EpCAM, ConfettiNeg,
- GSM7329523 EpCAM, ConfettiNeg, 6 EpCAM, ConfettiNeg,
- GSM7329524 EpCAM, ConfettiPos, 1 EpCAM, ConfettiPos,
- GSM7329525 EpCAM, ConfettiPos, 2 EpCAM, ConfettiPos,
- GSM7329526 EpCAM, ConfettiPos, 3 EpCAM, ConfettiPos,
- GSM7329527 EpCAM, ConfettiPos, 4 EpCAM, ConfettiPos,
- GSM7329528 EpCAM, ConfettiPos, 5 EpCAM, ConfettiPos,
- GSM7329529 EpCAM, ConfettiPos, 6 EpCAM, ConfettiPos,
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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.