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| license: mit |
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| # 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 |
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| - `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 |
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|
| - **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) |
