| --- |
| 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](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=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] |
