GEO series
Urine Cell-Free RNA versus Plasma Cell-Free RNA for Monitoring of Immune and Urinary Tract Complications
GSE261018
Homo sapiens (human)
RNA-seq (gene expression)
272 samples
Submitted 2025/03/06
Platform GPL24676Platform GPL30173
At a glance
RNA-seq (gene expression) · human · 272 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
- 272 samples: 97 × Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna vs 97 × Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrnaGroups 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
- Urine Cell-Free RNA vs Plasma Cell-Free RNA for Monitoring of Kidney Injury and Immune ComplicationsClinical chemistry · 2025
Summary (written by the submitters)
While it is well known that cell-free RNA (cfRNA) can be isolated from urine, the diagnostic potential of this urine cfRNA, especially in comparison to plasma cfRNA, remains underexplored. Here, we directly compared the utility of urine cfRNA and plasma cfRNA for the monitoring of systemic and urinary tract related complications. We analyzed 297 matched plasma and urine cfRNA isolates obtained from three cohorts of patients: Hematopoietic Stem Cell Transplant (HSCT) recipients, patients with acute kidney injury (AKI), and healthy volunteers.
Read the full summary ↓
The data highlight the unique cellular origins and properties of urinary and plasma RNA. Most importantly, we find that although plasma cfRNA is a superior analyte for monitoring immune and systemic complications, urinary cfRNA is more sensitive to complications of the urinary tract, including cell-type specific injury in the kidney. These findings highlight the potential of urine cfRNA as a novel analyte in diagnostic medicine.
Published in
Urine Cell-Free RNA vs Plasma Cell-Free RNA for Monitoring of Kidney Injury and Immune Complications
Mzava O, Agun GF, Loy CJ et al.
· Clinical chemistry 2025
· PMID 40796157
· doi:10.1093/clinchem/hvaf082
This dataset
Download · which file do I need?
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.
1 · Just have a look
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.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE261018_RAW.tar (it can run to tens of gigabytes).
3 · Start from the raw reads
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 PRJNA1084833. Searching any of these in the dataset finder brings you back here.
Study design
97 × Urine cell-free RNA, RNA seq gene counts for sample: gvhd-u-cfrna vs 97 × Plasma cell-free RNA, RNA seq gene counts for sample: gvhd_hct_cfrna
Supports a between-group comparison across 194 samples.
How we read this: 2 replicated groups read from 272 sample titles; they account for 194 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.
Samples in this study
- GSM8132419 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_1_61bp
- GSM8132420 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_2_61bp
- GSM8132421 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_3_61bp
- GSM8132422 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_4_61bp
- GSM8132423 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_6_61bp
- GSM8132424 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_7_61bp
- GSM8132425 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_9_61bp
- GSM8132426 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_10_61bp
- GSM8132427 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_11_61bp
- GSM8132428 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_13_61bp
- GSM8132429 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_14_61bp
- GSM8132430 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_15_61bp
- GSM8132431 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_16_61bp
- GSM8132432 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_17_61bp
- GSM8132433 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_18_61bp
- GSM8132434 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_19_61bp
- GSM8132435 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_21_61bp
- GSM8132436 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_23_61bp
- GSM8132437 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_24_61bp
- GSM8132438 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_25_61bp
- GSM8132439 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_26_61bp
- GSM8132440 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_27_61bp
- GSM8132441 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_29_61bp
- GSM8132442 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_30_61bp
- GSM8132443 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_31_61bp
- GSM8132444 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_33_61bp
- GSM8132445 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_35_61bp
- GSM8132446 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_36_61bp
- GSM8132447 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_39_61bp
- GSM8132448 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_40_61bp
- GSM8132449 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_41_61bp
- GSM8132450 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_42_61bp
- GSM8132451 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_43_61bp
- GSM8132452 Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_44_61bp
- GSM8132453 Urine cell-free RNA, RNA seq gene counts for sample: irb-u-cfrna-1-A
- GSM8132454 Urine cell-free RNA, RNA seq gene counts for sample: irb-u-cfrna-2-A
- GSM8132455 Urine cell-free RNA, RNA seq gene counts for sample: irb-u-cfrna-3-A
- GSM8132456 Urine cell-free RNA, RNA seq gene counts for sample: irb-u-cfrna-7-A
- GSM8132457 Urine cell-free RNA, RNA seq gene counts for sample: irb-u-cfrna-8-A
- GSM8132458 Plasma cell-free RNA, RNA seq gene counts for sample: aki_cfrna_52-trimmed
+ 232 more — browse all 272 samples with per-sample file links →
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Share this dataset
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.