Enteric neuronal GPR41-DHX9 signaling senses microbial metabolites to mediate the crosstalk between serotonergic neurons and intestinal stem cells
RNA-seq (gene expression) · mouse · 18 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
- 18 samples: 14 distinct titles, 2 of them repeatedGroups 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 GSE253995_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 PRJNA1068077 and SRA study SRP485418. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 18 sample titles: 14 distinct titles with little repetition. 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.
- GSM8031542 DW1
- GSM8031543 DW2
- GSM8031544 DW3
- GSM8031545 DK1
- GSM8031546 DK2
- GSM8031547 DK3
- GSM8031586 WT1-input
- GSM8031587 WT1-IP
- GSM8031588 WT2-input
- GSM8031589 WT2-IP
- GSM8031590 WT3-input
- GSM8031591 WT3-IP
- GSM8031592 KO1-input
- GSM8031593 KO1-IP
- GSM8031594 KO2-input
- GSM8031595 KO2-IP
- GSM8031596 KO3-input
- GSM8031597 KO3-IP
- 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 intestinal, microbial, crosstalk
- GSE283495 Intestinal epithelial cell diversity and function in respect to age, anatomical localization, and microbial exposure - the global transcriptome 29 samples shares intestinal, microbial
- 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
- GSE291179 MyD88-mediated signaling in intestinal fibroblasts regulates macrophage antimicrobial defense and prevents dysbiosis in the gut I 10 samples shares intestinal, microbial
- GSE242470 Intestinal Akkermansia muciniphila complements the efficacy of PD1 therapy in MAFLD-related hepatocellular carcinoma 16 samples shares intestinal
- GSE230307 NAC regulates metabolism and cell fate in intestinal stem cells 12 samples shares intestinal
- GSE318069 eIF4G2-mediated Translation Initiation of Histone Modifiers is Essential for Intestinal Stem Cell Maintenance and Differentiation 145 samples shares intestinal
- GSE294512 eIF4G2-mediated Translation Initiation of Histone Modifiers is Essential for Intestinal Stem Cell Maintenance and Differentiation [RNA-seq] 92 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.