Altas of gene expression in mice liver during liver regeneration process post 2/3 partial hepatectomy using RNA-seq
RNA-seq (gene expression) · mouse · 18 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
- 18 samples: 9 conditions, mostly in duplicateGroups 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.
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 GSE108449_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 PRJNA427311 and SRA study SRP127398. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 9 replicated groups read from 18 sample titles; they account for 18 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.
- GSM2898270 sham rep1 sham
- GSM2898271 sham rep2 sham
- GSM2898272 0.5h PH rep1 0.5h PH
- GSM2898273 0.5h PH rep2 0.5h PH
- GSM2898274 2h PH rep1 2h PH
- GSM2898275 2h PH rep2 2h PH
- GSM2898276 4h PH rep1 4h PH
- GSM2898277 4h PH rep2 4h PH
- GSM2898278 24h PH rep1 24h PH
- GSM2898279 24h PH rep2 24h PH
- GSM2898280 48h PH rep1 48h PH
- GSM2898281 48h PH rep2 48h PH
- GSM2898282 72h PH rep1 72h PH
- GSM2898283 72h PH rep2 72h PH
- GSM2898284 120h PH rep1 120h PH
- GSM2898285 120h PH rep2 120h PH
- GSM2898286 168h PH rep1 168h PH
- GSM2898287 168h PH rep2 168h PH
- 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 hepatectomy, partial, liver, post
- GSE233516 DNA dioxygenase Tet2 regulates liver regeneration after partial hepatectomy. 18 samples shares regeneration, hepatectomy, partial, liver
- GSE298695 Mechanosensing by endothelial Piezo1 promotes liver regeneration after partial hepatectomy via ATF2-ID1-Wnt2 pathway 16 samples shares regeneration, hepatectomy, partial, liver
- GSE282210 Transcriptome analysis of quiescent livers and regenerating livers after partial hepatectomy (PH) in young and aged mice 133 samples shares hepatectomy, partial, liver
- GSE328885 Liver transcriptomic response to partial hepatectomy in intestinal-specific SIRT1 knockout mice 34 samples shares hepatectomy, partial, liver
- GSE263879 Lipid influx enforces liver regeneration through the recruitment of CD36+ macrophages (scRNA-Seq and RNA-Seq) 10 samples shares regeneration, rna-seq, liver
- GSE166225 Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates [RNA-seq] 288 samples shares process, rna-seq
- GSE279388 Inactivation of Atp7b copper transporter in the intestinal epithelial cells is associated with altered lipid processing and cell growth machinery that are independent from hepatic copper accumulation and liver histology severity 76 samples shares process, liver
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.