Mouse enteric neurons control intestinal plasmacytoid dendritic cell function via serotonin-HTR7 signaling [Sep_Epi]
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 × SI epithelium of Tph2 WT vs 3 × SI epithelium of Tph2 KO vs 3 × LI epithelium of Tph2 WT vs 3 × LI epithelium of Tph2 KOGroups 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.
- Paper
- Mouse enteric neurons control intestinal plasmacytoid dendritic cell function via serotonin-HTR7 signalingNature communications · 2024
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 GSE227216_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 PRJNA944157 and SRA study SRP427029. 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.
- GSM7093288 SI epithelium of Tph2 WT 1 SI epithelium of Tph2 WT
- GSM7093289 SI epithelium of Tph2 WT 2 SI epithelium of Tph2 WT
- GSM7093290 SI epithelium of Tph2 WT 3 SI epithelium of Tph2 WT
- GSM7093291 SI epithelium of Tph2 KO 1 SI epithelium of Tph2 KO
- GSM7093292 SI epithelium of Tph2 KO 2 SI epithelium of Tph2 KO
- GSM7093293 SI epithelium of Tph2 KO 3 SI epithelium of Tph2 KO
- GSM7093294 LI epithelium of Tph2 WT 1 LI epithelium of Tph2 WT
- GSM7093295 LI epithelium of Tph2 WT 2 LI epithelium of Tph2 WT
- GSM7093296 LI epithelium of Tph2 WT 3 LI epithelium of Tph2 WT
- GSM7093297 LI epithelium of Tph2 KO 1 LI epithelium of Tph2 KO
- GSM7093298 LI epithelium of Tph2 KO 2 LI epithelium of Tph2 KO
- GSM7093299 LI epithelium of Tph2 KO 3 LI epithelium of Tph2 KO
- GSE304886 Intestinal plasmacytoid dendritic cells preferentially produce interferon lambda 11 samples shares plasmacytoid, intestinal, dendritic
- GSE296433 Engineered probiotics limit T-cell driven CNS autoimmunity by activating AHR-KLF4-FADS3 signaling in intestinal dendritic cells 40 samples shares intestinal, dendritic
- GSE252188 Tonic type I interferon signaling optimizes the antiviral function of plasmacytoid dendritic cells [Bulk RNA-seq] 15 samples shares plasmacytoid, dendritic
- GSE302271 Plasmacytoid dendritic cells are dispensable or detrimental in murine systemic or respiratory viral infections [RNA-Seq 2] 22 samples shares plasmacytoid, dendritic
- GSE302124 Plasmacytoid dendritic cells are dispensable or detrimental in murine systemic or respiratory viral infections [RNA-Seq 1] 18 samples shares plasmacytoid, dendritic
- GSE283007 Prior High Fiber Intake Impinges on the Cellular Responses of Mesenteric Adipose and Intestinal Tissues to Subsequent High Fat Feeding 16 samples shares intestinal, enteric
- GSE271298 Cohesin-mediated chromatin organization controls the differentiation and function of dendritic cells 103 samples shares dendritic, control
- GSE322757 IL-17RC signaling connects intestinal microbiota and neuroimmune interactions in atherosclerosis 42 samples shares intestinal
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.