Culturing of primary mouse hepatocytes is associated with major changes to the proteome and transcriptome
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: 12 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.
- Paper
- Hepatocyte dedifferentiation in 2D culture reveals extensive transcriptomic and proteomic rewiringHepatology communications · 2025
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 GSE280301_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 PRJNA1177797 and SRA study SRP540818. 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 12 sample titles: 12 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.
- GSM8594438 reaction_1_RNA
- GSM8594439 reaction_2_RNA
- GSM8594440 reaction_3_RNA
- GSM8594441 reaction_4_RNA
- GSM8594442 reaction_5_RNA
- GSM8594443 reaction_6_RNA
- GSM8594444 reaction_1_HTO
- GSM8594445 reaction_2_HTO
- GSM8594446 reaction_3_HTO
- GSM8594447 reaction_4_HTO
- GSM8594448 reaction_5_HTO
- GSM8594449 reaction_6_HTO
- GSE273058 Expression changes in mouse proximal tubules during primary culture 18 samples shares primary, changes
- GSE285689 Bile duct ligation (BDL)-induced changes on the gene expression of different primary cells in mice liver. 18 samples shares primary, changes
- GSE274374 Benzbromarone exacerbates high-fat-induced lipid accumulation in primary hepatocytes by activating PPARγ [OA] 12 samples shares hepatocytes, primary
- GSE276001 mRNA Sequencing Analysis of MCM7 Knockdown in Primary Hepatocytes Under IL-6 Stimulation 12 samples shares hepatocytes, primary
- GSE302714 RNA Sequencing of primary mouse hepatocytes treated with manganese (Mn) or insulin 12 samples shares hepatocytes, primary
- GSE26460 Expression data from primary hepatocytes isolated from miR-143DOX mice 6 samples shares hepatocytes, primary
- GSE269392 The key regulation of LncRNA MALAT1/miR-124-3p/PI3K axis during reprogramming of primary mouse hepatocytes into insulin-producing cells 4 samples shares hepatocytes, primary
- GSE225576 An atlas of the aging mouse transcriptome and proteome reveals the features of age-related post-transcriptional dysregulation 128 samples shares proteome
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.