Comparison of transcriptional changes in regenerating mice livers at baseline and 3-12 hours post 70% partial hepatectomy
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 × RNA-seq_Control vs 3 × RNA-seq_PHx3h vs 3 × RNA-seq_PHx6h vs 3 × RNA-seq_PHx12hGroups 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 GSE255995_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 PRJNA1077368 and SRA study SRP490063. 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.
- GSM8083944 RNA-seq_Control_1 RNA-seq_Control
- GSM8083945 RNA-seq_Control_2 RNA-seq_Control
- GSM8083946 RNA-seq_Control_3 RNA-seq_Control
- GSM8083947 RNA-seq_PHx3h_1 RNA-seq_PHx3h
- GSM8083948 RNA-seq_PHx3h_2 RNA-seq_PHx3h
- GSM8083949 RNA-seq_PHx3h_3 RNA-seq_PHx3h
- GSM8083950 RNA-seq_PHx6h_1 RNA-seq_PHx6h
- GSM8083951 RNA-seq_PHx6h_2 RNA-seq_PHx6h
- GSM8083952 RNA-seq_PHx6h_3 RNA-seq_PHx6h
- GSM8083953 RNA-seq_PHx12h_1 RNA-seq_PHx12h
- GSM8083954 RNA-seq_PHx12h_2 RNA-seq_PHx12h
- GSM8083955 RNA-seq_PHx12h_3 RNA-seq_PHx12h
- GSE256002 Comparison of transcriptional changes in regenerating mice livers at baseline and 24-48 hours post 70% partial hepatectomy with or without etomoxir treatment 27 samples shares regenerating, hepatectomy, comparison, baseline, changes, partial, livers, hours
- GSE282210 Transcriptome analysis of quiescent livers and regenerating livers after partial hepatectomy (PH) in young and aged mice 133 samples shares regenerating, hepatectomy, partial, livers
- GSE281923 Gene expression profiling by bulk RNAseq from the livers of wild-type mice and those with loss-of-function mutations in URI 48 hours after partial hepatectomy 8 samples shares hepatectomy, partial, livers, hours
- GSE255292 H3K27ac CUT&Tag of regenerating liver after 70% partial hepatectomy 4 samples shares regenerating, hepatectomy, partial
- GSE282998 Comparison of phenotypic and transcriptomic profiles between HFPO-DA and prototypical PPARα, PPARγ, and cytotoxic agents in wild-type and PPARα knockout mouse livers 192 samples shares comparison, livers
- GSE328885 Liver transcriptomic response to partial hepatectomy in intestinal-specific SIRT1 knockout mice 34 samples shares hepatectomy, partial
- GSE329873 Transcriptomic analysis of hepatocyte specific Eed knock out compared to wild type mice before and after partial hepatectomy 20 samples shares hepatectomy, partial
- GSE233516 DNA dioxygenase Tet2 regulates liver regeneration after partial hepatectomy. 18 samples shares hepatectomy, partial
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.