GEO series
Hepatic stellate cells regulate liver fatty acid utilization via plasmalemma vesicle-associated protein [bulk RNA-seq]
GSE246086
Mus musculus (mouse)
RNA-seq (gene expression)
46 samples
Submitted 2025/03/04
Platform GPL24247
At a glance
RNA-seq (gene expression) · mouse · 46 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
- 46 samples: 46 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
- Hepatic stellate cells regulate liver fatty acid utilization via plasmalemma vesicle-associated proteinCell metabolism · 2025
Summary (written by the submitters)
The liver is essential for normal fatty acid utilization during fasting. Circulating fatty acids are taken up by hepatocytes and esterified as triacylglycerols for either oxidative metabolization and ketogenesis or export. Whereas the regulation of fatty acid oxidation in hepatocytes is well understood, the uptake and retention of non-esterified fatty acids by hepatocytes is not.
Read the full summary ↓
Here, we show that murine hepatic stellate cells (HSCs) and their abundantly expressed plasmalemma vesicle-associated protein (PLVAP) control hepatic substrate preference for fasting energy metabolism. HSC-specific ablation of PLVAP in mice elevated hepatic insulin signaling and improved glucose tolerance. Fasted HSC PLVAP knockout mice showed suppressed hepatic fatty acid esterification to di- and triacylglycerols shifting fasting metabolism from fatty acid oxidation to reliance on carbohydrates. By super-resolution microscopy we localized HSC PLVAP to caveolae residing along the sinusoidal lumen supporting a role for HSCs and PLVAP-diaphragmed caveolae in normal fasting metabolism of the liver.
Published in
Hansen D, Jensen JER, Andersen CAT et al.
· Cell metabolism 2025
· PMID 40037362
· doi:10.1016/j.cmet.2025.01.022
This dataset
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.
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 GSE246086_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1031256 and SRA study SRP468021. Searching any of these in the dataset finder brings you back here.
Study design
46 samples, each with a distinct title — no replicated groups
Supports a case/control comparison: 22 samples read as cases, 24 as controls.
How we read this: Read from 46 sample titles: 46 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.
Samples in this study
- GSM7855277 Liver, bulk RNA-seq, chow diet, littermate control, rep A, (A422)
- GSM7855278 Liver, bulk RNA-seq, chow diet, littermate control, rep B, (A423)
- GSM7855279 Liver, bulk RNA-seq, chow diet, littermate control, rep C, (A424)
- GSM7855280 Liver, bulk RNA-seq, chow diet, littermate control, rep D, (A425)
- GSM7855281 Liver, bulk RNA-seq, chow diet, littermate control, rep E, (A426)
- GSM7855282 Liver, bulk RNA-seq, chow diet, littermate control, rep F, (A427)
- GSM7855283 Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep A, (A429)
- GSM7855284 Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep B, (A430)
- GSM7855285 Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep C, (A431)
- GSM7855286 Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep D, (A432)
- GSM7855287 Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep E, (A433)
- GSM7855288 Liver, bulk RNA-seq, chow diet, littermate control, rep A, (C377)
- GSM7855289 Liver, bulk RNA-seq, chow diet, littermate control, rep B, (C378)
- GSM7855290 Liver, bulk RNA-seq, chow diet, littermate control, rep C, (C379)
- GSM7855291 Liver, bulk RNA-seq, chow diet, littermate control, rep D, (C380)
- GSM7855292 Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep A, (C381)
- GSM7855293 Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep B, (C382)
- GSM7855294 Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep C, (C383)
- GSM7855295 Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep D, (C384)
- GSM7855296 Liver, bulk RNA-seq, chow diet, WT C57BL/6N, rep A, (C955)
- GSM7855297 Liver, bulk RNA-seq, chow diet, WT C57BL/6N, rep B, (C956)
- GSM7855298 Liver, bulk RNA-seq, chow diet, WT C57BL/6N, rep C, (C957)
- GSM7855299 Liver, bulk RNA-seq, chow diet, WT C57BL/6N, rep D, (C958)
- GSM7855300 Liver, bulk RNA-seq, chow diet, whole-body Cav1 knockout, rep A, (C959)
- GSM7855301 Liver, bulk RNA-seq, chow diet, whole-body Cav1 knockout, rep B, (C960)
- GSM7855302 Liver, bulk RNA-seq, chow diet, whole-body Cav1 knockout, rep C, (C961)
- GSM7855303 Liver, bulk RNA-seq, chow diet, whole-body Cav1 knockout, rep D, (C962)
- GSM8556048 Liver, bulk RNA-seq, western diet, littermate control, rep A
- GSM8556049 Liver, bulk RNA-seq, western diet, littermate control, rep B
- GSM8556050 Liver, bulk RNA-seq, western diet, littermate control, rep C
- GSM8556051 Liver, bulk RNA-seq, western diet, littermate control, rep D
- GSM8556052 Liver, bulk RNA-seq, western diet, littermate control, rep E
- GSM8556053 Liver, bulk RNA-seq, western diet, HSC Plvap knockout, rep A
- GSM8556054 Liver, bulk RNA-seq, western diet, HSC Plvap knockout, rep B
- GSM8556055 Liver, bulk RNA-seq, western diet, HSC Plvap knockout, rep C
- GSM8556056 Liver, bulk RNA-seq, western diet, HSC Plvap knockout, rep D
- GSM8556057 Liver, bulk RNA-seq, high-fat diet, littermate control, rep A
- GSM8556058 Liver, bulk RNA-seq, high-fat diet, littermate control, rep B
- GSM8556059 Liver, bulk RNA-seq, high-fat diet, littermate control, rep C
- GSM8556060 Liver, bulk RNA-seq, high-fat diet, littermate control, rep D
+ 6 more — browse all 46 samples with per-sample file links →
Datasets on a similar topic
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- GSE246088 Hepatic stellate cells regulate liver fatty acid utilization via plasmalemma vesicle-associated protein 52 samples shares vesicle-associated, utilization, plasmalemma, stellate, regulate, hepatic, protein
- GSE328089 Therapeutic Targeting of AREL1 in Hepatic Stellate Cells Attenuates MASH-related Liver Fibrosis [RNA-Seq] 8 samples shares stellate, hepatic, rna-seq
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- GSE231690 Widespread transmission of DNA supercoiling and selective topoisomerase utilization regulates torsional stress within the neuronal genome [RNA-Seq] 3 samples shares utilization, regulate, rna-seq
- GSE263080 RNA-sea of Smad4 wild-type or Smad4 knockout KPC PDAC organoids from monocultures or co-cultures with pancreatic stellate cells and RNA-seq of flow-sorted PSCs from the same co-cultures. 44 samples shares stellate, rna-seq
- GSE263081 RNA-sea of Smad4 wild-type or Smad4 knockout KvPC PDAC organoids from monocultures or co-cultures with pancreatic stellate cells and RNA-seq of flow-sorted PSCs from the same co-cultures. 35 samples shares stellate, rna-seq
- GSE256377 Hepatic stellate cells control liver zonation and function via R-spondin 3 [bulkRNAseq_mouse_HSCdepleted] 34 samples shares stellate, hepatic
Share this dataset
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.