Transcriptome profiles of neonatal mouse intestinal organoids with or without LPS sitimulation and tryptophan metabolites intervention
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 × Fibroblast, control, vs 3 × Fibroblast, LPS, vs 3 × Fibroblast, LPS_Indoles, vs 3 × Fibroblast, LPS_Indoles_CH223191,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.
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 GSE279880_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 PRJNA1175034 and SRA study SRP539614. 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.
- GSM8582488 Fibroblast, control, rep1 Fibroblast, control,
- GSM8582489 Fibroblast, control, rep2 Fibroblast, control,
- GSM8582490 Fibroblast, control, rep3 Fibroblast, control,
- GSM8582491 Fibroblast, LPS, rep1 Fibroblast, LPS,
- GSM8582492 Fibroblast, LPS, rep2 Fibroblast, LPS,
- GSM8582493 Fibroblast, LPS, rep3 Fibroblast, LPS,
- GSM8582494 Fibroblast, LPS_Indoles, rep1 Fibroblast, LPS_Indoles,
- GSM8582495 Fibroblast, LPS_Indoles, rep2 Fibroblast, LPS_Indoles,
- GSM8582496 Fibroblast, LPS_Indoles, rep3 Fibroblast, LPS_Indoles,
- GSM8582497 Fibroblast, LPS_Indoles_CH223191, rep1 Fibroblast, LPS_Indoles…
- GSM8582498 Fibroblast, LPS_Indoles_CH223191, rep2 Fibroblast, LPS_Indoles…
- GSM8582499 Fibroblast, LPS_Indoles_CH223191, rep3 Fibroblast, LPS_Indoles…
- GSE279881 Transcriptome profiles of neonatal intestinal organoids under fibroblast coculture with or without LPS sitimulation and tryptophan metabolites intervention 15 samples shares lps, sitimulation, intervention, metabolites, intestinal, tryptophan, organoids, profiles
- GSE279383 Transcriptome profiles of RAW264.7 cells under fibroblast coculture with or without LPS sitimulation and tryptophan metabolites intervention 24 samples shares lps, sitimulation, intervention, metabolites, tryptophan, profiles
- GSE278583 Effect of Drp1 inhibitor on gene expression profiles of RAW264.7 cells at 24 hours or 96 hours after LPS and IFN-γ stimulation 12 samples shares lps, profiles
- GSE253995 Enteric neuronal GPR41-DHX9 signaling senses microbial metabolites to mediate the crosstalk between serotonergic neurons and intestinal stem cells 18 samples shares metabolites, intestinal
- GSE332798 Transcriptomic profiling of morphine and LPS exposure across mouse brain regions 208 samples shares lps
- GSE181643 Oxygen-dependent changes and lysosome activity-dependent changes of gene expression in BMDM after LPS treatment 72 samples shares lps
- GSE295334 RNA sequencing data of leptomeningeal/perivascular CAMs and MG following LPS stimulation 8 weeks after repopulation 54 samples shares lps
- GSE277696 Role of endothelial SOCS3 in the transcriptional response to LPS 45 samples shares lps
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.