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README.md

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+# Data Card: DILGOM Whole-Blood Microarray Dataset (E-TABM-1036)
+
+## Summary
+
+Expression + sample metadata + feature metadata for E-TABM-1036, which
+profile whole-blood gene expression in a population-based cohort from
+the Helsinki/Vantaa area of Finland. Profiled on Illumina HumanHT-12 v3
+Expression BeadChip. This accession has **no obesity or metabolic-syndrome
+phenotype data**. These are the 'healthy' controls.
+
+## Source accession
+
+| Accession | N (SDRF rows) | Platform | Submitter |
+|---|---|---|---|
+| [E-TABM-1036](https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-TABM-1036) | 518 | Illumina HumanHT-12 v3 | Inouye (Wellcome Trust Sanger Institute) |
+
+
+## Files
+
+- `sample_metadata.parquet` — one row per sample: `sample_id`, `accession`, `age_band`, `sex`.
+  This is the full extent of usable per-sample metadata in the SDRF — see Notes.
+- `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`)
+- `expression/` — partitioned parquet dataset (by `accession`, for schema consistency with
+  other datasets in this collection even though there is only one accession here),
+  long format: `IlluminaID`, `sample_id`, `accession`, `value`
+
+## Expression value processing (from the accession's IDF)
+
+Per the submitter's own protocol description (`bioassay_data_transformation`
+protocol, P-TABM-5309):
+
+> *"Normalized intensities were calculated via quantile normalization of
+> the weighted-sums of the raw replicate intensities. Weighting was by
+> number of beads contributing to raw signal. Final intensities were
+> arrived at by a log2 transformation after quantile normalization."*
+
+RNA source: PAXgene Blood RNA Tubes, whole blood (per protocol
+P-TABM-5305), amplified via in vitro transcription (P-TABM-5306) and
+hybridized to HumanHT-12 v3 BeadChips (P-TABM-5307).
+
+
+## Provenance / reproducibility
+
+Data retrieved with `ArrayExpress::getAE()` against BioStudies (EBI), with
+probe annotation from Bioconductor's `illuminaHumanv3.db`. See
+[pull_dilgom.R](pull_dilgom.R)