Gene expression profile at single cell level of mouse liver in whole and fibrotic niche of the liver (scRNA-Seq)
Single-cell RNA-seq · mouse · 18 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Mus musculus (mouse)
- Samples
- 18 samples: 6 × OC, vs 5 × OF, vs 3 × YF,Groups 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 GSE276063_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1154629 and SRA study SRP529750. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 3 replicated groups read from 18 sample titles; they account for 14 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.
- GSM8490518 OC, replicate 1 OC,
- GSM8490519 OC, replicate 2 OC,
- GSM8490520 OC, replicate 3 OC,
- GSM8490521 OC, replicate 4 OC,
- GSM8490522 OC, replicate 5 OC,
- GSM8490523 OC, replicate 6 OC,
- GSM8490524 OF, replicate 1 OF,
- GSM8490525 OF, replicate 2 OF,
- GSM8490526 OF, replicate 3 OF,
- GSM8490527 OF, replicate 4 OF,
- GSM8490528 OF, replicate 5 OF,
- GSM8490529 YF, replicate 1 YF,
- GSM8490530 YF, replicate 2 YF,
- GSM8490531 YF, replicate 3 YF,
- GSM8618756 YC, replicate 1, scRNAseq
- GSM8618757 YC, replicate 2, scRNAseq
- GSM8618758 YC, replicate 3, scRNAseq
- GSM8618759 YF, replicate 1, scRNAseq
- GSE280373 Spatiotemporal dynamics of the cardioimmune niche during lesion repair [scRNA-seq] 28 samples shares scrna-seq, niche
- GSE274973 Mouse liver assembloids model periportal architecture and biliary fibrosis [scRNA-seq] 13 samples shares scrna-seq, liver
- GSE248386 ILC2 regulate a Pi16+ fibroblast progenitor niche in the pancreas (acute pancreatitis scRNA-seq) 10 samples shares scrna-seq, niche
- GSE264105 Plate-based scRNA-seq of plasma-positive microglia and plasma-negative microglia in young mice 1111 samples shares scrna-seq
- GSE271100 Stem cells tightly regulate dead cell clearance to maintain tissue fitness [scRNA-seq] 1037 samples shares scrna-seq
- GSE230260 Gene expression profile at single cell level of cells isolated from the bone fracture gap and un-injured bone marrow in mouse osteotomy models 15 samples shares level
- GSE326100 scRNA-seq of mouse cochlea organoid cells 768 samples shares scrna-seq
- GSE266918 RNA-seq expression analysis of liver, adipose, skeletal muscle, heart, and pancreatic islets from DO founder strain mice fed high-fat, high-sugar diet. [heart] 63 samples shares 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.