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| license: mit |
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| # Data Card: DILGOM Whole-Blood Microarray Dataset (E-TABM-1036) |
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|
| ## Summary |
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|
| 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 |
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|
| | 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) | |
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| ## Files |
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| - `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` |
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| ## Expression value processing (from the accession's IDF) |
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|
| 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). |
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| ## Provenance / reproducibility |
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| Data retrieved with `ArrayExpress::getAE()` against BioStudies (EBI), with |
| probe annotation from Bioconductor's `illuminaHumanv3.db`. See |
| [pull_dilgom.R](pull_dilgom.R) |
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