---
license: mit
---
# Data Card: Sepsis vs. SIRS Point-of-Care Biomarker Whole-Blood Microarray Dataset (GSE236713)

## Summary

Expression + sample metadata + feature metadata for GSE236713, a
multi-center UK study identifying transcriptional mRNA biomarkers to
discriminate sepsis from SIRS in adult ICU patients, profiled on the
Agilent SurePrint G3 Human GE v2 8x60K Microarray (GPL17077). Blood was
sampled at up to four timepoints (Day 1, Day 2, Day 5, and ICU discharge)
for patient groups, and once for healthy controls.

## Source accession

| Accession | N (samples) | N (patients) | Platform | Retrieval source |
|---|---|---|---|---|
| [GSE236713](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM7573957) | 447 | 194 | Agilent SurePrint G3 Human GE v2 8x60K, probe-name version (GPL17077) | NCBI GEO |

Cohort breakdown: 30 healthy controls, 93 SIRS (Out-of-Hospital Cardiac
Arrest, OOHCA), 124 abdominal sepsis, 200 pulmonary sepsis.

## Files

- `sample_metadata.parquet` — one row per sample: `sample_id`, `patient_id`, `timepoint` (`Day: 1`/`Day: 2`/`Day: 5`/`Day: Discharge`), `outcome` (`Died`/`Survived`), `disease` (`Control`/`SIRS`/`Sepsis`), `disease_type` (`Healthy`/`OOHCA`/`Abdominal`/`Pulmonary`), `sex`
- `feature_metadata.parquet` — one row per probe (`feature_id`): Agilent's own platform annotation table, retrieved directly from GEO's GPL17077 record (no dedicated Bioconductor annotation package exists for this array design — confirmed via multiple Bioconductor support threads spanning several years, none reporting a resolution)
- `expression.parquet` — single file, long format: `feature_id`, `sample_id`, `value`

## Sample metadata field notes

- **Not every patient has all four timepoints.** Of 194 patients: 55 have
  1 sample, 48 have 2, 68 have 3, 23 have 4. Timepoints were missed due to
  patient death, ICU discharge, or other events, per the accession's
  design description. Healthy controls were sampled once and recorded as
  `Day: 1` only.
- **`outcome`** is `Died` (91 samples) or `Survived` (356 samples).
- **`disease`**/**`disease_type`** together describe both severity tier
  and clinical subtype — `disease_type` is not a further breakdown of
  `disease` independent of it; each `disease` value maps to exactly one
  `disease_type` (Control→Healthy, SIRS→OOHCA, Sepsis→{Abdominal,
  Pulmonary}).

## Expression value processing

Per the accession, expression values are **normalized signal intensity**.
Independently confirmed as already log-scale: the standard log-detection
heuristic (99th percentile and range of values) returned `FALSE`,
indicating no further transformation was needed or applied. Values in
`expression.parquet` are exactly as deposited.

## Provenance / reproducibility

See [pull_gse236713.R](pull_gse236713.R)