ILC2 regulate a Pi16+ fibroblast progenitor niche in the pancreas (acute pancreatitis scRNA-seq)
Single-cell RNA-seq · mouse · 10 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
- 10 samples: 3 × PBS, vs 3 × AP d3, vs 2 × AP d1, vs 2 × AP d7,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.
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 GSE248386_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 PRJNA1043656 and SRA study SRP473286. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 4 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.
- GSM7912852 PBS, rep 1 PBS,
- GSM7912853 PBS, rep 2 PBS,
- GSM7912854 PBS, rep 3 PBS,
- GSM7912855 AP d1, rep 1 AP d1,
- GSM7912856 AP d1, rep 2 AP d1,
- GSM7912857 AP d3, rep 1 AP d3,
- GSM7912858 AP d3, rep 2 AP d3,
- GSM7912859 AP d3, rep 3 AP d3,
- GSM7912860 AP d7, rep 1 AP d7,
- GSM7912861 AP d7, rep 2 AP d7,
- GSE248387 ILC2 regulate a Pi16+ fibroblast progenitor niche in the pancreas 32 samples shares ilc2, pi16, fibroblast, progenitor, regulate, pancreas
- GSE285771 Orai1 in pancreatic ductal cells mediates pancreas-intestinal crosstalk in experimental acute pancreatitis via the secretion of antimicrobial peptide REG3B in pancreatic juice 18 samples shares pancreatitis, pancreas
- GSE261166 Transcription factor 21 regulates cardiac myofibroblast formation and fibrosis [RNA-Seq] 16 samples shares fibroblast, regulate
- GSE277228 Changing dynamics of the fibroblast differentiation hierarchy during mammary gland morphogenesis and tumorigenesis [scRNA-Seq I] 13 samples shares fibroblast, scrna-seq
- GSE308848 Targeting AEBP1 to mitigate pro-tumor activity of cancer-associated fibroblasts and increase therapeutic efficacy to anti-PD-1 [scRNA-Seq] 12 samples shares fibroblast, scrna-seq
- GSE287483 Competing dynamic gene regulatory networks involved in fibroblast reprogramming to haematopoietic progenitor cells [RNA-Seq] 12 samples shares fibroblast, progenitor
- GSE312968 Reversible Fibroblast Trajectories Regulated by MR Underlie Diastolic Dysfunction 12 samples shares fibroblast, regulate
- GSE313761 Single-cell screens identify ADAM12 as a fibroblast checkpoint impeding anti-tumor immunity - scRNA-seq of Adam12CKO Mouse Model CD45- cells 11 samples shares fibroblast, scrna-seq
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.