Data Card: Pediatric SIRS/Sepsis/Septic Shock Spectrum Whole-Blood Microarray Dataset (GSE13904)

Summary

Expression + sample metadata + feature metadata for GSE13904, a whole-blood gene expression study measuring genome-level expression profiles across the pediatric systemic inflammatory response syndrome (SIRS), sepsis, and septic shock spectrum, profiled on the Affymetrix HG-U133 Plus 2.0 Array (GPL570). Prospective observational cohort of children ≤10 years of age, sampled at day 1 and, for a subset still meeting sepsis criteria or whose SIRS had resolved, day 3.

Source accession

Accession	N (samples)	N (patients)	Platform	Retrieval source
GSE13904	227	186	Affymetrix HG-U133 Plus 2.0 (GPL570), 54,675 probes	NCBI GEO

Patient/sample breakdown by category:

Day 1 — 18 control, 22 SIRS, 32 sepsis, 67 septic shock (139 total; verified directly against the associated publication's day-1 breakdown, an exact match).

Day 3 — 5 SIRS, 24 SIRS resolved, 20 sepsis, 39 septic shock (88 total; 139 day-1 + 88 day-3 = 227, matching the full deposited sample count).

Files

• sample_metadata.parquet — one row per sample: sample_id, timepoint, clinical_status
• feature_metadata.parquet — one row per probe (PROBEID): annotation from hgu133plus2.db (SYMBOL, ENTREZID, ENSEMBL, GENENAME, UNIPROT)
• expression.parquet — single file (only one accession), long format: PROBEID, sample_id, accession, value

Sample metadata field notes

• clinical_status is timepoint-dependent, not a fixed per-patient label — it reflects a patient's status at that draw. Of 186 total patients, 145 were sampled at day 1 only and 41 at both day 1 and day 3. For those 41, day-1 → day-3 status changed as follows:

  Day 1	Day 3	N patients
  SIRS	SIRS	2
  SIRS	SIRS resolved	1
  SIRS	Sepsis	1
  Sepsis	Sepsis	3
  Sepsis	SIRS resolved	4
  Septic Shock	Septic Shock	19
  Septic Shock	Sepsis	3
  Septic Shock	SIRS resolved	7
  Septic Shock	SIRS	1

  SIRS resolved only occurs as a day-3 value (12 of 41 followed-up patients). Do not collapse clinical_status to one label per patient without deciding explicitly which timepoint you want.

• No age or sex data exists for this accession. None provided in the accession sample level metadata

Expression value processing

The expression values in the accession are 'normalized to a control', but not placed on a log scale. They are log2 transformed before being saved to this repo.

Provenance / reproducibility

see pull_gse13904.R