A conserved HAND2-BMP5-SMAD1/5/9 axis drives hepatic stellate cell activation and extracellular matrix overproduction in multiple fibrotic etiologies
RNA-seq (gene expression) · human · 10 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
- Homo sapiens (human)
- Samples
- 10 samples: 5 × Control vs 5 × BMP5Groups 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 GSE341139_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 PRJNA1499629 and SRA study SRP720651. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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.
- GSM9900727 Control rep1 Control
- GSM9900728 Control rep2 Control
- GSM9900729 Control rep3 Control
- GSM9900730 Control rep4 Control
- GSM9900731 Control rep5 Control
- GSM9900732 BMP5 rep1 BMP5
- GSM9900733 BMP5 rep2 BMP5
- GSM9900734 BMP5 rep3 BMP5
- GSM9900735 BMP5 rep4 BMP5
- GSM9900736 BMP5 rep5 BMP5
- GSE341616 A conserved HAND2-HAND2_OE-SMAD1/5/9 axis drives hepatic stellate cell activation and extracellular matrix overproduction in multiple fibrotic etiologies 5 samples shares overproduction, extracellular, activation, etiologies, conserved, stellate, multiple
- GSE276915 Hepatic stellate cell single cell atlas reveals a highly similar activation process across liver disease aetiologies 10 samples shares activation, etiologies, stellate
- GSE274680 Inflammation and lymphocyte activation during longitudinal progression to rheumatoid arthritis in at-risk individuals 243 samples shares activation
- GSE318645 Dual Immune Checkpoint Blockade Induces Distinct Systemic and Intratumoral Immune Activation in Recurrent Glioblastoma 226 samples shares activation
- GSE254732 Inhibition of PCSK9 with evolocumab modulates lipoproteins and monocyte activation in high-risk ASCVD subjects 215 samples shares activation
- GSE297395 Extracellular vesicles and their RNA cargo facilitate bidirectional cross-kingdom communication between human and bacterial cells [RNA-Seq] 105 samples shares extracellular
- GSE273700 Whole transcriptome analysis reveals T cell signaling activation in septic patients with thrombocytopenia 104 samples shares activation
- GSE208732 Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer [RNA-seq] 102 samples shares extracellular
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.