DNA dioxygenase Tet2 regulates liver regeneration after partial hepatectomy.
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: 18 samples, each with a distinct title — no replicated groupsGroups 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 GSE233516_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 PRJNA976469 and SRA study SRP439683. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 18 sample titles: 18 distinct titles with little repetition. 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.
- GSM7429790 Primary hepatocyes1 [PH1]
- GSM7429791 Primary hepatocyes2 [PH2]
- GSM7429792 Primary hepatocyes3 [PH3]
- GSM7429793 Primary hepatocyes+Bobcat339-1 [BC1]
- GSM7429794 Primary hepatocyes+Bobcat339-2 [BC2]
- GSM7429795 Primary hepatocyes+Bobcat339-3 [BC3]
- GSM7429796 Primary hepatocyes1+4-Octyl Itaconate-1 [ITA1]
- GSM7429797 Primary hepatocyes1+4-Octyl Itaconate-2 [ITA2]
- GSM7429798 Primary hepatocyes1+4-Octyl Itaconate-3 [ITA3]
- GSM7429799 0h after PHx -Liver macrophages 1 [M0_1]
- GSM7429800 0h after PHx -Liver macrophages 2 [M0_2]
- GSM7429801 0h after PHx -Liver macrophages 3 [M0_3]
- GSM7429802 24h after PHx -Liver macrophages 1 [M24_1]
- GSM7429803 24h after PHx -Liver macrophages 2 [M24_2]
- GSM7429804 24h after PHx -Liver macrophages 3 [M24_3]
- GSM7429805 48h after PHx -Liver macrophages 1 [M48_1]
- GSM7429806 48h after PHx -Liver macrophages 2 [M48_2]
- GSM7429807 48h after PHx -Liver macrophages 3 [M48_3]
- GSE298695 Mechanosensing by endothelial Piezo1 promotes liver regeneration after partial hepatectomy via ATF2-ID1-Wnt2 pathway 16 samples shares regeneration, hepatectomy, partial, liver
- GSE108449 Altas of gene expression in mice liver during liver regeneration process post 2/3 partial hepatectomy using RNA-seq 18 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
- 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
- GSE283252 Acetylcholine derived from B lymphocytes controls liver regeneration 26 samples shares regeneration, liver
- GSE286997 FGF2 Mediated USP42-PPAR Axis Activation Ameliorates Liver Oxidative Damage and Promotes Regeneration 12 samples shares regeneration, liver
- GSE263879 Lipid influx enforces liver regeneration through the recruitment of CD36+ macrophages (scRNA-Seq and RNA-Seq) 10 samples shares regeneration, 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.