Pathogen-induced tissue-resident memory TH17 (TRM17) cells amplify autoimmune kidney disease
Single-cell RNA-seq · human · 18 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Homo sapiens (human)
- 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.
- Paper
- Pathogen-induced tissue-resident memory T(H)17 (T(RM)17) cells amplify autoimmune kidney diseaseScience immunology · 2020
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 GSE270533_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1127463 and SRA study SRP515591. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 12 samples read as cases, 6 as controls.
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.
- GSM8346282 Patient 01, Kidney
- GSM8346283 Patient 02, Kidney
- GSM8346284 Patient 03, Kidney
- GSM8346285 Patient 04, Kidney
- GSM8346286 Patient 05, Kidney
- GSM8346287 Patient 06, Kidney
- GSM8346288 Control 01, Kidney
- GSM8346289 Control 02, Kidney
- GSM8346290 Control 03, Kidney
- GSM8346291 Patient 01, Blood
- GSM8346292 Patient 02, Blood
- GSM8346293 Patient 03, Blood
- GSM8346294 Patient 04, Blood
- GSM8346295 Patient 05, Blood
- GSM8346296 Patient 06, Blood
- GSM8346297 Control 01, Blood
- GSM8346298 Control 02, Blood
- GSM8346299 Control 03, Blood
- GSE247264 Single-cell analysis reveals clonal expansions of pro-inflammatory tissue-resident memory Th17 cells in Crohn's disease 22 samples shares th17, tissue-resident, memory
- GSE249197 Tissue-Resident Memory T Cells in Human Kidney Transplants have alloreactive potential 8 samples shares tissue-resident, memory, kidney
- GSE290921 CD4+ tissue resident memory Th17 cells drive IL-17A-mediated joint pathology in Spondyloarthritis 6 samples shares th17, memory
- GSE200996 Tissue-resident Memory and Circulating T cells are Early Responders to Pre-surgical Cancer Immunotherapy 204 samples shares tissue-resident, memory
- GSE90730 Tissue-resident memory features are linked to the magnitude of cytotoxic T cell responses in human lung cancer 109 samples shares tissue-resident, memory
- GSE305372 Human lungs maintain tissue-resident memory T cells against a broad spectrum of pathogens. 91 samples shares tissue-resident, memory
- GSE90728 Tissue-resident memory features are linked to the magnitude of cytotoxic T cell responses in human lung cancer [NSCLC] 68 samples shares tissue-resident, memory
- GSE90729 Tissue-resident memory features are linked to the magnitude of cytotoxic T cell responses in human lung cancer [HNSCC] 41 samples shares tissue-resident, memory
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.