mRNA profiles of DNT cells in primary biliary cholangitis patients
RNA-seq (gene expression) · human · 19 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
- 19 samples: 6 × DNT cells, HC vs 5 × DNT cells, PBC_U vs 4 × DNT cells, PBC vs 4 × DNT cells, PBC_naiveGroups 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 GSE138888_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 PRJNA577687 and SRA study SRP225754. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 19 samples.
How we read this: 4 replicated groups read from 19 sample titles; they account for 19 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.
- GSM4121300 DNT cells, HC_1 DNT cells, HC
- GSM4121301 DNT cells, HC_2 DNT cells, HC
- GSM4121302 DNT cells, HC_3 DNT cells, HC
- GSM4121303 DNT cells, HC_4 DNT cells, HC
- GSM4121304 DNT cells, HC_5 DNT cells, HC
- GSM4121305 DNT cells, HC_6 DNT cells, HC
- GSM4121306 DNT cells, PBC_R_1 DNT cells, PBC
- GSM4121307 DNT cells, PBC_R_2 DNT cells, PBC
- GSM4121308 DNT cells, PBC_R_3 DNT cells, PBC
- GSM4121309 DNT cells, PBC_R_4 DNT cells, PBC
- GSM4121310 DNT cells, PBC_UR_1 DNT cells, PBC_U
- GSM4121311 DNT cells, PBC_UR_2 DNT cells, PBC_U
- GSM4121312 DNT cells, PBC_UR_3 DNT cells, PBC_U
- GSM4121313 DNT cells, PBC_UR_4 DNT cells, PBC_U
- GSM4121314 DNT cells, PBC_UR_5 DNT cells, PBC_U
- GSM4121315 DNT cells, PBC_naive_1 DNT cells, PBC_naive
- GSM4121316 DNT cells, PBC_naive_2 DNT cells, PBC_naive
- GSM4121317 DNT cells, PBC_naive_3 DNT cells, PBC_naive
- GSM4121318 DNT cells, PBC_naive_4 DNT cells, PBC_naive
- GSE304352 Transcriptome analysis of liver tissue from patients with Autoimmune Hepatitis, Primary Biliary Cholangitis, and Chronic Hepatitis B 11 samples shares cholangitis, primary, biliary
- GSE231432 HSC-derived exosomal miR-122- 5p inhibits EMT and fibrosis of intrahepatic biliary epithelial cells to alleviate primary biliary cholangitis 24 samples shares cholangitis, primary, biliary
- GSE294300 Single-cell gene expression profiles of cells from primary colorectal cancer and adjacent normal tissue [scRNA-Seq] 36 samples shares profiles, primary
- GSE314342 Genome-scale perturb-seq in primary human CD4+ T cells reveals genes regulating T cell programs and human immune traits. 577 samples shares primary
- GSE277906 Expression profiles of human cumulus cells from patients with PCOS and non-PCOS 40 samples shares profiles
- GSE297742 Bulk RNA-seq of primary tumor biopsy samples from prostate adenocarcinoma patients 234 samples shares primary
- GSE306264 Transcriptional profiling of Hutchinson-Gilford Progeria patients identifies primary target pathways of the disease-causing progerin protein 96 samples shares primary
- GSE271961 Integrated electrophysiological and genomic profiles of single cells reveal spiking tumor cells in human glioma [Patch-Seq] 95 samples shares profiles
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.