---
license: mit
---
# 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.parquet` — 518 samples x 48,803 probes
  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)