Data Card: MARS Sepsis Blood Genomic Endotype Whole-Blood Microarray Dataset (GSE65682)

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