license: mit
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 amortality_28dvalue. - 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_controlfeature_metadata.parquet— one row per probe (PROBEID): annotation fromhgu219.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