| --- |
| license: mit |
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| # Data Card: MARS Sepsis Blood Genomic Endotype Whole-Blood Microarray Dataset (GSE65682) |
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|
| ## Summary |
|
|
| Expression + sample metadata + feature metadata for GSE65682, the |
| Molecular Diagnosis and Risk of Sepsis (MARS) study, profiling the |
| whole-blood leukocyte transcriptome of critically ill ICU patients to |
| distinguish infectious sepsis (community-acquired pneumonia [CAP], |
| hospital-acquired pneumonia [HAP]) from non-infectious causes of critical |
| illness (no-CAP controls), and to classify patients into molecular |
| "endotypes." Profiled on the Affymetrix HG-U219 Array (GPL13667). PAXgene |
| blood RNA was collected at ICU admission and, for a subset, later in ICU |
| stay. |
|
|
| ## Source accession |
|
|
| | Accession | N (samples) | Platform | Retrieval source | |
| |---|---|---|---| |
| | GSE65682 | 802 | Affymetrix HG-U219 (GPL13667), 24,646 probes | NCBI GEO | |
|
|
| This series bundles several independent, only partially-overlapping |
| sub-studies rather than one uniform cohort — each of the variables below |
| is populated for a different subset of the 802 samples, not a shared |
| disease-state axis: |
|
|
| - **Endotype/mortality** (479 samples: 263 discovery + 216 validation) — `endotype_cohort`, `endotype_class` (Mars1–4), `mortality_28d`, `time_to_event_28d`. Confirmed: every endotype-classified sample has a `mortality_28d` value. |
| - **ICU-acquired infection** (388 samples) — `icu_acquired_infection`, with a smaller paired subset (`icu_acquired_infection_paired`, 69 samples). |
| - **Pneumonia diagnosis** (225 samples: cap/hap/no-cap) — `pneumonia_diagnosis`. |
| - **Thrombocytopenia** (99 samples, graded A–D) — `thrombocytopenia`. |
| - **Diabetes mellitus** (410 samples) — `diabetes_mellitus`. |
| - **Abdominal sepsis / GI controls** (93 samples) — `abdominal_sepsis_or_control`. |
| - **Healthy controls** are flagged via `healthy_control` (logical). |
|
|
| Most fields are the literal string `"NA"` (or genuinely absent) outside |
| their relevant sub-study's sample set, not missing-at-random — treat each |
| variable's non-NA subset as its own analysis population. |
|
|
| ## Files |
|
|
| - `sample_metadata.parquet` — one row per sample: `sample_id`, `title_identifier1`, `title_identifier2`, `healthy_control`, `sex`, `age`, `pneumonia_diagnosis`, `thrombocytopenia`, `endotype_cohort`, `endotype_class`, `mortality_28d`, `time_to_event_28d`, `icu_acquired_infection`, `icu_acquired_infection_paired`, `diabetes_mellitus`, `abdominal_sepsis_or_control` |
| - `feature_metadata.parquet` — one row per probe (`PROBEID`): annotation from `hgu219.db` (`SYMBOL`, `ENTREZID`, `ENSEMBL`, `GENENAME`, `UNIPROT`). Confirmed 100% probe-ID match against the package's keyspace (24,646/24,646). |
| - `expression.parquet` — single file, long format: `PROBEID`, `sample_id`, `value` |
|
|
| ## Expression value processing |
|
|
| Values are **RMA-normalized, log2-transformed signal intensity**, as |
| deposited by the submitter. Confirmed already log-scale via the standard |
| detection heuristic; no further transformation applied. |
|
|
| ## Provenance / reproducibility |
|
|
| See [pull_gse65682.R](pull_gse65682.R) |
