A small intestinal bile acid modulates the gut microbiome to improve host metabolic phenotypes following bariatric surgery
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: 5 × 0mgKg vs 5 × 10mgKgGroups 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
- A small intestinal bile acid modulates the gut microbiome to improve host metabolic phenotypes following bariatric surgeryCell host & microbe · 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 GSE262065_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 PRJNA1090115 and SRA study SRP496736. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 2 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.
- GSM8156882 0mgKg_3 0mgKg
- GSM8156883 0mgKg_4 0mgKg
- GSM8156884 0mgKg_7 0mgKg
- GSM8156885 0mgKg_11 0mgKg
- GSM8156886 0mgKg_12 0mgKg
- GSM8156887 10mgKg_3 10mgKg
- GSM8156888 10mgKg_4 10mgKg
- GSM8156889 10mgKg_6 10mgKg
- GSM8156890 10mgKg_7 10mgKg
- GSM8156891 10mgKg_10 10mgKg
- GSE272353 Genetic context modulates aging and degeneration in the murine retina 201 samples shares modulates
- GSE278548 Metabolic modeling reveals the aging-associated decline of host-microbiome metabolic interactions in mice 119 samples shares microbiome
- GSE293180 Analysis of Host and Microbiome Responses to Antibiotics Reveals Microbiota-Independent Effects on Gut Immune Response [multiabx] 97 samples shares microbiome
- GSE246617 Cerebral vascular transcriptome profiling reveals intermittent fasting modulates chronic cerebral hypoperfusion-induced disease pathways. 78 samples shares modulates
- GSE310244 Dynamic Resilience: Stress Phenotypes and Their Impact on Opioid-Taking Behavior, Brain Activity, and Gene Expression 68 samples shares phenotypes
- GSE151088 miR-375 Regulates Intestinal Crypt Cell Landscape, Proliferation, and Regenerative Capacity 54 samples shares intestinal
- GSE282129 Small intestinal lymph node identity is defined by medullary stromal cells in humans and mice [Sorted_lns_macrophages_RNAseq] 45 samples shares intestinal
- 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.