Hepatic stellate cells control liver zonation and function via R-spondin 3 [bulkRNAseq_mouse_HSCdepleted]
RNA-seq (gene expression) · mouse · 34 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
- 34 samples: 34 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 control liver zonation, size and functions via R-spondin 3Nature · 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 GSE256377_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 PRJNA1079305 and SRA study SRP491094. 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 34 sample titles: 34 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.
- GSM8096408 RSCY-3, Control for HSC depleted_1
- GSM8096409 RSCY-4, Control for HSC depleted_2
- GSM8096410 RSCY-5, Control for HSC depleted_3
- GSM8096411 RSCY-6, HSC depleted_1
- GSM8096412 RSCY-7, HSC depleted_2
- GSM8096413 RSCY-8, HSC depleted_3
- GSM8582319 AS_Age_C_1, Aged control_1
- GSM8582320 AS_Age_C_2, Aged control_2
- GSM8582321 AS_Age_C_3, Aged control_3
- GSM8582322 AS_Age_C_4, Aged control_4
- GSM8582323 AS_Age_C_5, Aged control_5
- GSM8582324 AS_Age_R_1, Aged Rspo3 KO HSC_1
- GSM8582325 AS_Age_R_2, Aged Rspo3 KO HSC_2
- GSM8582326 AS_Age_R_3, Aged Rspo3 KO HSC_3
- GSM8582327 AS_Age_R_4, Aged Rspo3 KO HSC_4
- GSM8582328 AS_Age_R_5, Aged Rspo3 KO HSC_5
- GSM8582329 AS_Endo_C_1, Control for Rspo3 KO EC_1
- GSM8582330 AS_Endo_C_2, Control for Rspo3 KO EC_2
- GSM8582331 AS_Endo_C_3, Control for Rspo3 KO EC_3
- GSM8582332 AS_Endo_C_4, Control for Rspo3 KO EC_4
- GSM8582333 AS_Endo_R_1, Rspo3 KO EC_1
- GSM8582334 AS_Endo_R_2, Rspo3 KO EC_2
- GSM8582335 AS_Endo_R_3, Rspo3 KO EC_3
- GSM8582336 AS_Endo_R_4, Rspo3 KO EC_4
- GSM8619583 AR001, Rspo3 KO HSC_1
- GSM8619584 AR002, Rspo3 KO HSC_2
- GSM8619585 AR003, Rspo3 KO HSC_3
- GSM8619586 AR004, Control for Rspo3 KO HSC_1
- GSM8619587 AR005, Control for Rspo3 KO HSC_2
- GSM8619588 AR006, Control for Rspo3 KO HSC_3
- GSM8619589 AR007, Control for Rspo3 KO HSC_4
- GSM8619590 AR008, Rspo3 KO HSC_4
- GSM8619591 AR009, Control for Rspo3 KO HSC_5
- GSM8619592 AR010, Rspo3 KO HSC_5
- GSE246088 Hepatic stellate cells regulate liver fatty acid utilization via plasmalemma vesicle-associated protein 52 samples shares stellate, hepatic, liver
- GSE246086 Hepatic stellate cells regulate liver fatty acid utilization via plasmalemma vesicle-associated protein [bulk RNA-seq] 46 samples shares stellate, hepatic, liver
- GSE304977 Core clock pharmacological control in the mouse hepatic stellate cell (HSC) EMS404 24 samples shares stellate, hepatic, control
- GSE304664 Core clock genetic control in the mouse hepatic stellate cell (HSC) EMS404 12 samples shares stellate, hepatic, control
- GSE270404 Foxd1 expression identifies a distinct subset of hepatic stellate cells involved in liver fibrosis 12 samples shares stellate, hepatic, liver
- GSE294603 Purification protocol of hypertrophied hepatic stellate cells from CDAHFD mice liver for their transcriptomic characterization 10 samples shares stellate, hepatic, liver
- GSE245857 Hepatic stellate cell-derived thrombospondin-2 as a novel therapeutic target for liver fibrosis 8 samples shares stellate, hepatic, liver
- GSE313667 Lack of phosphoenolpyruvate carboxykinase 1 in hepatic stellate cells causes liver fibrosis by fueling tricarboxylic acid cycle and increasing glycolysis 8 samples shares stellate, hepatic, 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.