Human milk oligosaccharide 2’-fucosyllactose and lacto-n-neo-tetraose attenuate early-weaning-induced intestinal barrier dysfunction via gut microbiota modulation in mice
RNA-seq (gene expression) · mouse · 25 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
- 25 samples: 5 conditions, mostly with about 5 replicates eachGroups 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 GSE303393_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 PRJNA1295196 and SRA study SRP602901. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 25 samples.
How we read this: 5 replicated groups read from 25 sample titles; they account for 25 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.
- GSM9125227 Jejunum,Control,1 Jejunum,Control,
- GSM9125228 Jejunum,Control,2 Jejunum,Control,
- GSM9125229 Jejunum,Control,3 Jejunum,Control,
- GSM9125230 Jejunum,Control,4 Jejunum,Control,
- GSM9125231 Jejunum,Control,5 Jejunum,Control,
- GSM9125232 Jejunum,Weaned,1 Jejunum,Weaned,
- GSM9125233 Jejunum,Weaned,2 Jejunum,Weaned,
- GSM9125234 Jejunum,Weaned,3 Jejunum,Weaned,
- GSM9125235 Jejunum,Weaned,4 Jejunum,Weaned,
- GSM9125236 Jejunum,Weaned,5 Jejunum,Weaned,
- GSM9125237 Jejunum,HMOs,1 Jejunum,HMOs,
- GSM9125238 Jejunum,HMOs,2 Jejunum,HMOs,
- GSM9125239 Jejunum,HMOs,3 Jejunum,HMOs,
- GSM9125240 Jejunum,HMOs,4 Jejunum,HMOs,
- GSM9125241 Jejunum,HMOs,5 Jejunum,HMOs,
- GSM9125242 Jejunum,FL,1 Jejunum,FL,
- GSM9125243 Jejunum,FL,2 Jejunum,FL,
- GSM9125244 Jejunum,FL,3 Jejunum,FL,
- GSM9125245 Jejunum,FL,4 Jejunum,FL,
- GSM9125246 Jejunum,FL,5 Jejunum,FL,
- GSM9125247 Jejunum,LNnT,1 Jejunum,LNnT,
- GSM9125248 Jejunum,LNnT,2 Jejunum,LNnT,
- GSM9125249 Jejunum,LNnT,3 Jejunum,LNnT,
- GSM9125250 Jejunum,LNnT,4 Jejunum,LNnT,
- GSM9125251 Jejunum,LNnT,5 Jejunum,LNnT,
- GSE280377 Transactivation of EGF receptor in intestinal epithelial cells by 2’-fucosyllactose mediates prevention of colitis in adulthood 6 samples shares fucosyllactose, intestinal
- GSE168730 The Human Milk Oligosaccharide 3'Sialyllactose Promotes Selective Modulation of Inflammation and Reduces Atherosclerosis Development in Mice 55 samples shares oligosaccharide, modulation
- GSE312987 Effects of dietary human milk oligosaccharides (HMO) and Trichuiris muris (Tm) infection on the caecum transcriptome in mice 30 samples shares oligosaccharide
- GSE310711 Bifidobacteria infantis and human milk oligosaccharides have independent effects on immune response and amino acid metabolism in germ-free mouse models 15 samples shares oligosaccharide
- GSE167999 The Human Milk Oligosaccharide 3’Sialyllactose Promotes Inflammation Resolution and Reduces Atherosclerosis Development in Mice 12 samples shares oligosaccharide
- GSE186412 The Human Milk Oligosaccharide 3’Sialyllactose Promotes Inflammation Resolution and Reduces Atherosclerosis Development in Mice 9 samples shares oligosaccharide
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.