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Primary cilia as a targetable node between biliary injury, senescence and regeneration

GSE220722 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/07/12 Platform GPL32941Platform GPL30172
At a glance

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 × Biliary epithelial cells PC competent, vs 3 × Biliary epithelial cells PC depleted, vs 3 × Biliary epithelial cells 0hrs hypoxia vs 3 × Biliary epithelial cells 12hrs hypoxiaGroups 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
Primary cilia as a targetable node between biliary injury, senescence and regeneration in liver transplantationJournal of hepatology · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Primary cilia as a targetable node between biliary injury, senescence and regeneration in liver transplantation
Esser H, Kilpatrick AM, Man TY et al. · Journal of hepatology 2024 · PMID 38879173 · doi:10.1016/j.jhep.2024.06.002
This dataset
Open GSE220722 in finder → Find more RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE220722_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA911227 and SRA study SRP412518. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38879173) ↗
Study design
3 × Biliary epithelial cells PC competent, vs 3 × Biliary epithelial cells PC depleted, vs 3 × Biliary epithelial cells 0hrs hypoxia vs 3 × Biliary epithelial cells 12hrs hypoxia

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.

Samples in this study
Datasets on a similar topic

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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.