Gene expression profile of human liver MAIT cells from patients with biliary atresia
RNA-seq (gene expression) · human · 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
- Homo sapiens (human)
- Samples
- 10 samples: 6 × BA vs 4 × HBGroups 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
- Mucosal-associated invariant T cells promote ductular reaction through amphiregulin in biliary atresiaEBioMedicine · 2024
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 GSE217466_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 PRJNA899068. 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.
- GSM6720088 BA-1 BA
- GSM6720091 BA-2 BA
- GSM6720093 BA-3 BA
- GSM6720095 BA-4 BA
- GSM6720099 BA-5 BA
- GSM6720103 BA-6 BA
- GSM6720106 HB-1 HB
- GSM6720110 HB-2 HB
- GSM6720114 HB-3 HB
- GSM6720116 HB-4 HB
- GSE304352 Transcriptome analysis of liver tissue from patients with Autoimmune Hepatitis, Primary Biliary Cholangitis, and Chronic Hepatitis B 11 samples shares biliary, liver
- GSE317449 Effect of depletion of TSPAN6 on Biliary Epithelial Cells with and without LPS stimulation mirroring liver disease. 20 samples shares biliary, liver
- GSE176189 Integrative single-cell and spatial transcriptomic analyses identify a pathogenic cholangiocyte niche and TNFRSF12A as therapeutic target for biliary atresia 36 samples shares biliary, atresia
- GSE223075 Next Generation Sequencing facilitates to identify the differential expression genes of sorted conventional CD8+ T cells and MAIT cells 35 samples shares mait
- GSE304585 MAIT and other innate-like T cells integrate adaptive immune responses to modulate interval-dependent reactogenicity to mRNA vaccines 259 samples shares mait
- GSE320009 Synergistic role of riboflavin-auxotrophic Enterococcus for MR1 expression and in-tra-tumoral mucosal associated invariant T (MAIT) cell activation 18 samples shares mait
- GSE263614 Gene expression profiling of human livers during normothermic machine perfusion 206 samples shares liver
- GSE270795 IL-23 tunes inflammatory functions of human MAIT cells 27 samples shares mait
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.