A post-translational regulatory map of chronic antigen-driven human T cell dysfunction
RNA-seq (gene expression) · human · 15 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
- 15 samples: 5 conditions, mostly in triplicateGroups 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 GSE294111_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 PRJNA1248406 and SRA study SRP577417. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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.
- GSM8898834 Activated,Day2,Rep1 Activated,Day2,
- GSM8898835 Activated,Day2,Rep2 Activated,Day2,
- GSM8898836 Activated,Day2,Rep3 Activated,Day2,
- GSM8898837 Acute,Day4,Rep1 Acute,Day4,
- GSM8898838 Acute,Day4,Rep2 Acute,Day4,
- GSM8898839 Acute,Day4,Rep3 Acute,Day4,
- GSM8898840 Chronic,Day4,Rep1 Chronic,Day4,
- GSM8898841 Chronic,Day4,Rep2 Chronic,Day4,
- GSM8898842 Chronic,Day4,Rep3 Chronic,Day4,
- GSM8898843 Acute,Day8,Rep1 Acute,Day8,
- GSM8898844 Acute,Day8,Rep2 Acute,Day8,
- GSM8898845 Acute,Day8,Rep3 Acute,Day8,
- GSM8898846 Chronic,Day8,Rep1 Chronic,Day8,
- GSM8898847 Chronic,Day8,Rep2 Chronic,Day8,
- GSM8898848 Chronic,Day8,Rep3 Chronic,Day8,
- GSE261258 Human regulatory memory B cells defined by expression of TIM-1 and TIGIT are dysfunctional in Multiple Sclerosis. 89 samples shares dysfunction, regulatory
- GSE298578 Single cell RNA profiling of blood CD4+ T cells identifies distinct helper and dysfunctional regulatory clusters in children with SLE (5' PBMC validation dataset) 14 samples shares dysfunction, regulatory
- GSE274114 Metabolic dysfunction-associated steatohepatitis reduces interferon and macrophage liver gene signatures in chronic HBV patients 39 samples shares dysfunction, chronic
- GSE289881 Exploring fibroblast activation protein as an early biomarker in chronic lung allograft dysfunction 10 samples shares dysfunction, chronic
- GSE285515 NKG2D blockade impairs cytotoxic CD8+ tissue resident memory T cell accumulation and attenuates severity of chronic lung allograft dysfunction after transplantation 15 samples shares dysfunction, chronic
- GSE278330 Systemic IL-23 blockade downregulates IL-23 receptor-expressing Type 17 T-cell subsets and upregulates regulatory gene expression in myeloid cells in human psoriasis skin 63 samples shares regulatory
- GSE233539 A human iPSC-derived multilineage liver organoid model containing Kupffer cells to study human sepsis-associated liver dysfunction 22 samples shares dysfunction
- GSE224392 Immunotherapies that repolarize macrophages and regulatory T cells enhance the effect of chemotherapy in high-grade serous ovarian cancer (Human) 21 samples shares regulatory
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.