Nociceptor neurons direct fibroblasts via a PACAP-VIPR2 axis to drive IL-11 production and colon healing
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 3 × Sorted fibroblast from wild-typre mice,Vehicle, vs 3 × Sorted fibroblast from wild-typre mice,PACAP, vs 3 × Sorted fibroblast from Vipr2-KO mice,Vehicle, vs 3 × Sorted fibroblast from Vipr2-KO mice,PACAP,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 GSE302394_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 PRJNA1290321 and SRA study SRP600142. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9103389 Sorted fibroblast from wild-typre mice,Vehicle,rep1 Sorted fibroblast from …
- GSM9103390 Sorted fibroblast from wild-typre mice,Vehicle,rep2 Sorted fibroblast from …
- GSM9103391 Sorted fibroblast from wild-typre mice,Vehicle,rep3 Sorted fibroblast from …
- GSM9103392 Sorted fibroblast from wild-typre mice,PACAP,rep1 Sorted fibroblast from …
- GSM9103393 Sorted fibroblast from wild-typre mice,PACAP,rep2 Sorted fibroblast from …
- GSM9103394 Sorted fibroblast from wild-typre mice,PACAP,rep3 Sorted fibroblast from …
- GSM9103395 Sorted fibroblast from Vipr2-KO mice,Vehicle,rep1 Sorted fibroblast from …
- GSM9103396 Sorted fibroblast from Vipr2-KO mice,Vehicle,rep2 Sorted fibroblast from …
- GSM9103397 Sorted fibroblast from Vipr2-KO mice,Vehicle,rep3 Sorted fibroblast from …
- GSM9103398 Sorted fibroblast from Vipr2-KO mice,PACAP,rep1 Sorted fibroblast from …
- GSM9103399 Sorted fibroblast from Vipr2-KO mice,PACAP,rep2 Sorted fibroblast from …
- GSM9103400 Sorted fibroblast from Vipr2-KO mice,PACAP,rep3 Sorted fibroblast from …
- GSE284092 Myocardial Fibroblasts are a Primary Source High Molecular Weight Hyaluronan Production in the Failing Heart 20 samples shares fibroblasts, production
- GSE284546 Myocardial Fibroblasts are a Primary Source High Molecular Weight Hyaluronan Production in the Failing Heart [RNASeq_Has2_knockout] 16 samples shares fibroblasts, production
- GSE68715 Global transcriptional analysis of mouse fibroblasts, chemically-induced neurons (neuron-like cells) from mouse fibroblasts and mouse primary cortical neurons by RNA-seq 15 samples shares fibroblasts, neurons
- GSE264265 MECHANISMS UNDERLYING THE DIRECT PROGRAMMING OF MOUSE EMBRYONIC FIBROBLASTS TO THYMIC EPITHELIAL CELLS BY FOXN1 [RNA-seq] 13 samples shares fibroblasts, direct
- GSE248850 Developmental origins of fibroblasts determine their scarring potential in wound healing 12 samples shares fibroblasts, healing
- GSE229916 Pericytes and perivascular fibroblasts contribute to central nervous system fibrosis in a region dependent manner 832 samples shares fibroblasts
- GSE273413 Adipose stem cells are sexually dimorphic cells with dual roles as preadipocytes and resident fibroblasts [FACS_pgWAT_iWAT_ASC] 143 samples shares fibroblasts
- GSE274992 Splenic fibroblasts control marginal zone B-cell movement and function via two distinct Notch2-dependent regulatory programs 119 samples shares fibroblasts
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.