ILC2 regulate a Pi16+ fibroblast progenitor niche in the pancreas (coculture bulk RNA-seq)
RNA-seq (gene expression) · mouse · 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
- Mus musculus (mouse)
- Samples
- 10 samples: 4 × FB_monoculture vs 3 × WT_coculture vs 3 × IL13KO_cocultureGroups 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 GSE248383_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 PRJNA1043649 and SRA study SRP473297. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 3 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.
- GSM7912826 FB_monoculture_1 FB_monoculture
- GSM7912827 FB_monoculture_2 FB_monoculture
- GSM7912828 FB_monoculture_3 FB_monoculture
- GSM7912829 FB_monoculture_4 FB_monoculture
- GSM7912830 WT_coculture_1 WT_coculture
- GSM7912831 WT_coculture_2 WT_coculture
- GSM7912832 WT_coculture_3 WT_coculture
- GSM7912833 IL13KO_coculture_1 IL13KO_coculture
- GSM7912834 IL13KO_coculture_2 IL13KO_coculture
- GSM7912835 IL13KO_coculture_3 IL13KO_coculture
- GSE248386 ILC2 regulate a Pi16+ fibroblast progenitor niche in the pancreas (acute pancreatitis scRNA-seq) 10 samples shares ilc2, pi16, fibroblast, progenitor, regulate, pancreas, rna-seq
- GSE248387 ILC2 regulate a Pi16+ fibroblast progenitor niche in the pancreas 32 samples shares ilc2, pi16, fibroblast, progenitor, regulate, pancreas
- GSE261166 Transcription factor 21 regulates cardiac myofibroblast formation and fibrosis [RNA-Seq] 16 samples shares fibroblast, regulate, rna-seq
- GSE287483 Competing dynamic gene regulatory networks involved in fibroblast reprogramming to haematopoietic progenitor cells [RNA-Seq] 12 samples shares fibroblast, progenitor, rna-seq
- GSE326762 Fate mapping reveals a prenatal-to-neonatal wave of ILC2s with a history of Cd3g expression - RNA-Seq 35 samples shares ilc2, rna-seq
- GSE278980 Single-cell screens identify ADAM12 as a fibroblast checkpoint impeding anti-tumor immunity - RNA-seq of C57BL/6 murine models 32 samples shares fibroblast, rna-seq
- GSE291075 The transcription factor NFIL3 drives innate lymphoid cell specification from lymphoid progenitors [RNA-seq - ex vivo, Nfil3] 27 samples shares progenitor, rna-seq
- GSE279386 Tp53 and Tet2 mutations cooperatively transform progenitors (RNA-Seq) 24 samples shares progenitor, rna-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.