GEO series
Plasma Cell-free RNA Signatures of Inflammatory Syndromes in Children
GSE255555
Homo sapiens (human)
RNA-seq (gene expression)
370 samples
Submitted 2024/09/11
Platform GPL18573
At a glance
RNA-seq (gene expression) · human · 370 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
- 370 samples: 133 × Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd vs 111 × Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_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
- Plasma cell-free RNA signatures of inflammatory syndromes in childrenProceedings of the National Academy of Sciences of the United States of America · 2024
Summary (written by the submitters)
Inflammatory syndromes, including those caused by infection, are a major cause of hospital admissions among children and are often misdiagnosed because of a lack of advanced molecular diagnostic tools. In this study, we explored the utility of circulating cell-free RNA (cfRNA) in plasma as an analyte for the differential diagnosis and characterization of pediatric inflammatory syndromes.
Read the full summary ↓
We profiled cfRNA in 370 plasma samples from pediatric patients with a range of inflammatory conditions, including Kawasaki disease (KD), Multisystem Inflammatory Syndrome in Children (MIS-C), viral infections and bacterial infections. We developed machine learning models based on these cfRNA profiles, which effectively differentiated KD from MIS-C — two conditions presenting with overlapping symptoms — with high performance (Test Area Under the Curve (AUC) = 0.97). We further extended this methodology into a multiclass machine learning framework that achieved 81% accuracy in distinguishing among KD, MIS-C, viral, and bacterial infections. We further demonstrated that cfRNA profiles can be used to quantify injury to specific tissues and organs, including the liver, heart, endothelium, nervous system, and the upper respiratory tract. Overall, this study identified cfRNA as a versatile analyte for the differential diagnosis and characterization of a wide range of pediatric inflammatory syndromes.
Published in
Loy CJ, Servellita V, Sotomayor-Gonzalez A et al.
· Proceedings of the National Academy of Sciences of the United States of America 2024
· PMID 39240972
· doi:10.1073/pnas.2403897121
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 GSE255555_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 PRJNA1075432. Searching any of these in the dataset finder brings you back here.
Study design
133 × Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd vs 111 × Plasma cell-free RNA, RNA seq gene counts for sample: prevail_cu_cfrna
Supports a between-group comparison across 244 samples.
How we read this: 2 replicated groups read from 370 sample titles; they account for 244 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
- GSM8074716 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_202_trimmed
- GSM8074717 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_128 Plasma cell-free RNA, R…
- GSM8074718 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_121 Plasma cell-free RNA, R…
- GSM8074719 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_47 Plasma cell-free RNA, R…
- GSM8074720 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_207_trimmed
- GSM8074721 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_218_trimmed
- GSM8074722 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_129 Plasma cell-free RNA, R…
- GSM8074723 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_222_trimmed
- GSM8074724 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_55 Plasma cell-free RNA, R…
- GSM8074725 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_212_trimmed
- GSM8074726 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_130 Plasma cell-free RNA, R…
- GSM8074727 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_56 Plasma cell-free RNA, R…
- GSM8074728 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_203_trimmed
- GSM8074729 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_57 Plasma cell-free RNA, R…
- GSM8074730 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_208_trimmed
- GSM8074731 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_235_trimmed
- GSM8074732 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_131 Plasma cell-free RNA, R…
- GSM8074733 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_193_trimmed
- GSM8074734 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_229_trimmed
- GSM8074735 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_213_trimmed
- GSM8074736 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_117 Plasma cell-free RNA, R…
- GSM8074737 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_58 Plasma cell-free RNA, R…
- GSM8074738 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_59 Plasma cell-free RNA, R…
- GSM8074739 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_132 Plasma cell-free RNA, R…
- GSM8074740 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_122 Plasma cell-free RNA, R…
- GSM8074741 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_118 Plasma cell-free RNA, R…
- GSM8074742 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_60 Plasma cell-free RNA, R…
- GSM8074743 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_123 Plasma cell-free RNA, R…
- GSM8074744 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_231_trimmed
- GSM8074745 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_133 Plasma cell-free RNA, R…
- GSM8074746 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_183_trimmed
- GSM8074747 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_61 Plasma cell-free RNA, R…
- GSM8074748 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_134 Plasma cell-free RNA, R…
- GSM8074749 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_94 Plasma cell-free RNA, R…
- GSM8074750 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_10 Plasma cell-free RNA, R…
- GSM8074751 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_33 Plasma cell-free RNA, R…
- GSM8074752 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_18 Plasma cell-free RNA, R…
- GSM8074753 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_62 Plasma cell-free RNA, R…
- GSM8074754 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_137 Plasma cell-free RNA, R…
- GSM8074755 Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_223_trimmed
+ 330 more — browse all 370 samples with per-sample file links →
Datasets on a similar topic
- GSE296680 Using plasma cell-free mRNA to profile immune response and myocardial damage in immune checkpoint inhibitor-induced myocarditis 26 samples shares cell-free, plasma
- GSE280708 Detection and monitoring of translocation renal cell carcinoma via plasma cell-free epigenomic profiling 161 samples shares cell-free, plasma
- GSE292059 Inflammatory Epithelial and Macrophage Pathways Underlie Residual Asthma Exacerbations in Urban Children Treated with Mepolizumab 965 samples shares children
- GSE291471 Integrative blood profiling uncovers inflammatory network signatures in high-altitude pulmonary edema 83 samples shares signatures
- GSE243625 Inflammatory transcriptomic signatures and cell type compositions in inflamed and non-inflamed colonic mucosa of ulcerative colitis 45 samples shares signatures
- GSE316742 SGLT2 inhibition reverses metabolic and inflammatory kidney signatures in youth with type 1 diabetes 27 samples shares signatures
- GSE300879 Identification of replicative aging and inflammatory aging signatures via whole-genome CRISPRi screens 16 samples shares signatures
- GSE286042 Transcriptomic and Proteomic Signatures Following AS03-adjuvanted Influenza A/H7N9 Vaccine 1232 samples shares signatures
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.