Weaning-Driven Gut Microbiome Shapes Intestinal Stem Cell Epigenetics to Train Immunological Memory (RNA-seq)
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: 18 samples, each with a distinct title — no replicated groupsGroups 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 GSE275418_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 PRJNA1150633 and SRA study SRP527913. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 18 sample titles: 18 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.
- GSM8476564 SPF_replicate_1_LDf170DCo
- GSM8476565 SPF_replicate_2_LDf168DCo
- GSM8476566 SPF_replicate_3_LDf178DCo
- GSM8476567 SPF_replicate_4_LDf179DCo
- GSM8476568 SPF_replicate_5_LDf21708DCo
- GSM8476569 SPF_replicate_6_LDf8595DCo
- GSM8476570 SPF_replicate_1_LDf42Co
- GSM8476571 SPF_replicate_2_LDf1021Co
- GSM8476572 GF_replicate_1_A328329DCo
- GSM8476573 GF_replicate_2_A332333DCo
- GSM8476574 GF_replicate_3_A86712DCo
- GSM8476575 GF_replicate_4_A005DCo
- GSM8476576 GF_replicate_5_A457DCo
- GSM8476577 GF_replicate_6_A458DCo
- GSM8476578 GF_replicate_7_A460DCo
- GSM8476579 GF_replicate_8_A462DCo
- GSM8476580 GF_replicate_1_A7802Co
- GSM9500030 GF_replicate_2_GFP100_CO_S
- GSE272841 Life-long microbiome rejuvenation improves intestinal metabolism and inflammaging in mice [bulk RNA-seq] 39 samples shares microbiome, intestinal, rna-seq
- GSE85154 The spectrum and regulatory landscapes of intestinal innate lymphoid cells are shaped by the microbiome (RNA-Seq) 24 samples shares microbiome, intestinal, rna-seq
- GSE272842 Life-long microbiome rejuvenation improves intestinal metabolism and inflammaging in mice [scRNA-seq] 12 samples shares microbiome, intestinal, rna-seq
- GSE313357 Hippocampal estrogen levels, receptor types and epigenetics contribute to sex-specific memory-vulnerabilities to concurrent acute stresses [RNA-Seq] 9 samples shares epigenetics, rna-seq, memory
- GSE306576 Fasting primes small intestinal regeneration after damage via a microbiome-metabolite-chromatin axis [RNA-seq] 4 samples shares microbiome, intestinal, rna-seq
- GSE229963 The intestinal clock controls host’s metabolic response to diet by driving intestinal metabolic functions and the fiber-dependent microbiome 48 samples shares microbiome, intestinal
- GSE341280 Systematic identification of age-related microbiome metabolites that impact the brain - mouse brain RNA-seq 28 samples shares microbiome, rna-seq
- GSE268945 Dietary fiber inulin enables intestinal microbiome to clear fructose and protect the host 24 samples shares microbiome, 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.