README.md

metadata

license: mit
task_categories:
  - other
tags:
  - transcriptomics
  - microarray
  - illumina
  - whole-blood
  - population-cohort

Data Card: SHIP-TREND Whole-Blood Microarray Dataset (GSE36382)

Summary

Expression + feature metadata for SHIP-TREND, a population-based whole-blood gene expression dataset from the SHIP-TREND (Study of Health in Pomerania). 991 samples, all self-reported as White European ethnicity from North-Eastern Germany.

This is used in the SepsisStratifier work as a healthy control set.

Source accession

Accession	Platform	N (samples)	Retrieval source
GSE36382	Illumina HumanHT-12 V3.0 (GPL6947)	991	NCBI GEO, via GEOquery::getGEO()

Files

• 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 annotation pipeline used for DILGOM, since both are on the v3 platform.
• expression/ — partitioned parquet dataset (by accession, for schema consistency with other datasets in this collection), long format: IlluminaID, sample_id, accession, value.
• No sample_metadata.parquet for this dataset. Phenotype data is restricted and only available upon valid request.

Expression value processing

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

Provenance / reproducibility

See [pull_GSE26282.R]