Trained immunity suppression determines kidney allograft survival
RNA-seq (gene expression) · human · 12 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
- 12 samples: 6 × PBMC, high, vs 6 × PBMC, low,Groups 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
- Trained immunity suppression determines kidney allograft survivalAmerican journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons · 2024
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 GSE280787_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 PRJNA1180533 and SRA study SRP542370. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 2 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8605810 PBMC, high, 196 PBMC, high,
- GSM8605811 PBMC, high, 197 PBMC, high,
- GSM8605812 PBMC, high, 220 PBMC, high,
- GSM8605813 PBMC, high, 226 PBMC, high,
- GSM8605814 PBMC, low, 229 PBMC, low,
- GSM8605815 PBMC, low, 230 PBMC, low,
- GSM8605816 PBMC, high, 233 PBMC, high,
- GSM8605817 PBMC, low, 242 PBMC, low,
- GSM8605818 PBMC, low, 243 PBMC, low,
- GSM8605819 PBMC, low, 244 PBMC, low,
- GSM8605820 PBMC, high, 250 PBMC, high,
- GSM8605821 PBMC, low, 378 PBMC, low,
- GSE328649 Lineage 2-Beijing Mycobacterium tuberculosis strains suppress BCG-trained innate immunity early after infection 39 samples shares immunity, trained
- GSE262098 Transcriptomes during monocyte-to-macrophage differentiation and BCG induced trained immunity in vitro 21 samples shares immunity, trained
- GSE303481 Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease 15 samples shares determines, kidney
- GSE323311 Human Macrophages Encode Stimulus-Specific Information of Prior Exposures Through Trained Immunity 48 samples shares immunity, trained
- GSE262097 Remodeling of Histone 3 Lysine 18 lactylation (H3K18lac) in monocytes-to-macrophage differentiation and induction of Trained Immunity by BCG in vitro 37 samples shares immunity, trained
- GSE276544 MVA-based SARS-CoV-2 vaccine candidates encoding different spike protein conformations induce distinct early transcriptional responses which may impact subsequent adaptive immunity 305 samples shares immunity
- GSE247531 Single-cell landscape of hematopoiesis and immunological responses in patients with severe aplastic anemia treated with immunosuppression and eltrombopag 182 samples shares suppression
- GSE239843 Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst [RNA-seq I] 134 samples shares suppression
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.