Benchmarking urinary cell transcriptomes for noninvasive differentiation of BK polyomavirus-associated nephropathy from T cell-mediated rejection
RNA-seq (gene expression) · human · 11 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
- 11 samples: 7 × urine RNA, BKVN-P, vs 4 × urine RNA, BKVN-N,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
- Benchmarking urinary cell transcriptomes for noninvasive differentiation of BK polyomavirus-associated nephropathy from T cell-mediated rejectionJCI insight · 2026
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 GSE312597_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 PRJNA1374274 and SRA study SRP651555. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 11 samples.
How we read this: 2 replicated groups read from 11 sample titles; they account for 11 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.
- GSM9349896 urine RNA, BKVN-N, 1 urine RNA, BKVN-N,
- GSM9349897 urine RNA, BKVN-N, 2 urine RNA, BKVN-N,
- GSM9349898 urine RNA, BKVN-N, 3 urine RNA, BKVN-N,
- GSM9349899 urine RNA, BKVN-N, 4 urine RNA, BKVN-N,
- GSM9349900 urine RNA, BKVN-P, 1 urine RNA, BKVN-P,
- GSM9349901 urine RNA, BKVN-P, 2 urine RNA, BKVN-P,
- GSM9349902 urine RNA, BKVN-P, 3 urine RNA, BKVN-P,
- GSM9349903 urine RNA, BKVN-P, 4 urine RNA, BKVN-P,
- GSM9349904 urine RNA, BKVN-P, 5 urine RNA, BKVN-P,
- GSM9349905 urine RNA, BKVN-P, 6 urine RNA, BKVN-P,
- GSM9349906 urine RNA, BKVN-P, 7 urine RNA, BKVN-P,
- GSE287697 Clazakizumab treatment effects on peripheral blood and kidney transcriptomes in chronic antibody-mediated rejection 58 samples shares transcriptomes, rejection
- GSE166239 Partial epithelial-to-mesenchymal transition (EMT) and T cell-mediated inflammation in hypertensive and diabetic nephropathy 18 samples shares cell-mediated, nephropathy
- GSE81861 Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors 1220 samples shares transcriptomes
- GSE205672 Transcriptomes of human PBMCs and monocytes in sepsis patients 460 samples shares transcriptomes
- GSE302316 Neutrophil transcriptomes in blunt traumatic injury 80 samples shares transcriptomes
- GSE232391 Cell-mediated cytotoxicity surrounding the brain in spinal muscular atrophy 47 samples shares cell-mediated
- GSE157198 Next Generation Sequencing Facilitates Quantitative Analysis of HIV Elite controller, HIV ART, HIV ART-naive and healthy control Transcriptomes 44 samples shares transcriptomes
- GSE294985 Transcriptomes of human whole blood cells in sepsis patients 40 samples shares transcriptomes
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.