Data Card: Parnell Sepsis Serial-Sampling Whole-Blood Microarray Dataset (GSE54514)

Summary

Expression + sample metadata + feature metadata for GSE54514, a whole-blood gene expression study assessing immune dysfunction in critically ill septic patients over the course of ICU admission. Blood was sampled daily for up to 5 days from septic patients and healthy controls.

Source accession

Accession	N (samples)	N (patients)	Platform	Retrieval source
GSE54514	163	54 (18 healthy, 10 sepsis nonsurvivor, 26 sepsis survivor)	Illumina HT-12 v3 (48,804 probes per accession description)	NCBI GEO

Files

• sample_metadata.parquet — one row per sample: sample_id, accession, group_id, day, disease_status, sex, age, apache_ii, neutrophil_proportion, site_of_infection
• feature_metadata.parquet — one row per probe (IlluminaID): annotation from illuminaHumanv3.db (SYMBOL, ENTREZID, ENSEMBL, GENENAME, UNIPROT) plus reannotation QC fields from the package's internal ExtraInfo table (ProbeQuality, CodingZone, GenomicLocation, SecondMatches, OtherGenomicMatches, RepeatMask, OverlappingSNP, ProbeSequence) — same pipeline used for DILGOM and SHIP-TREND.
• expression.parquet — single file long format: IlluminaID, sample_id, value

Expression value processing

Per the accession description, expression values are quantile-normalized and log2-transformed signal intensity.

Provenance / reproducibility

see pull_gse54514.R