Omics Overview
Methylation Normalization
Molecular Networks
Brain xQTL Serve
Multi-layered omics datasets are generated from biospecimens donated by ROS and MAP participants, which include genetics, epigenetics, and next generation RNA-seq.
Other layers of omics data are generated from frozen dorsolateral prefrontal cortical tissue.
- Genotype data are generated from peripheral blood mononuclear cells or frozen brain using Affymetrix or the Illumina Omniquad express gene chips. Genotypes are imputed on ~7 million SNPs using the 1000 (1K) Genomes Project data as reference.
- Epigenome-wide data include DNA methylation profiles with the Illumina Infinium HumanMethylation450 beadset, which covers approximately half a million discrete CpG dinucleotides.
- Profiles of histone acetylation (H3K9Ac) are generated using chromatin immunoprecipitation followed by Illumina-seq, and over 100,000 peaks of acetylation have been annotated from each brain.
- MicroRNA data are generated using the NanoString nCounter miRNA expression assay, resulting in 309 miRNA. miRNA expression data are available at both gene and isoform levels.
- RNA-seq library preparation is performed on the Broad Institute's Genomics Platform, and sequencing is conducted on the Illumina HiSeq with 101bp paired-end reads, achieving coverage of at least 75M reads.
- Metabolomic data is generated from brain tissue and serum samples using the Biocrates Absolute/DQ p180 kit which quantifies over 180 metabolites from 5 analyte groups: acylcarnitines, amino acids, biogenic amines, glycerophospholipids, and sphingolipids. Brain bile acid data is generated separately. Bile acid-free matrix (BAFM) is used to prepare bile acid calibrators. Bile acid concentrations are quantified by UPLC and processed using TargetLynx applications manager.
- Lipidomic data is generated from brain tissue and serum samples using liquid chromatography-mass spectrometry.
Please refer to each individual dataset below for details on tissue preparation and data processing pipelines.
See also: Omics participant identifiers
Genotyping
| Type | Description | Sample Size | More Info / Request Data |
|---|---|---|---|
| SNP (Affymetrix) | Single Nucleotide Polymorphisms | 1709 |
Genotypes @ Synapse Imputed 1k @ Synapse |
| SNP (Illumina) | Single Nucleotide Polymorphisms | 382 |
Genotypes @ Synapse Imputed 1k @ Synapse |
| WES | Whole Exome Sequencing | 783 |
ADSP dbGaP |
| WGS | Whole Genome Sequencing | 1425 |
Synapse Synapse |
Epigenetics
| Type | Description | Sample Size | More Info / Request Data |
|---|---|---|---|
| H3K9Ac | Histone acetylation marks (ChIP-seq) | 714 | Synapse |
| miRNA | MicroRNA expression | 702 | Synapse |
| 5 mc | DNA methylation 5-methylcytosine | 740 | Synapse |
| 5 hmC | DNA methylation 5-hydroxymethylcytosine | 1060 | Request |
| ATAC Seq | Chromatin Conformation | In Process |
Gene Expression (mRNA)
| Type | Description | Sample Size | More Info / Request Data |
|---|---|---|---|
| RNAseq | Next-generation RNA sequencing | 1417 | Request, Synapse |
| RNA microarray | RNA microarray-measured gene expression | 492 | Synapse |
| snRNAseq PFC | Single-nucleus RNA-seq of prefrontal cortex | 48 | Synapse |
| RNAseq PFC microglia | RNA-seq of prefrontal cortex microglia | 10 | Synapse |
| scRNAseq PFC microglia | Single-cell RNA-seq of prefrontal cortex | 13 | Synapse |
| RNAseq monocyte | RNA-seq of peripheral blood mononuclear cell | 558 | Synapse |
| snRNAseq | Single-nucleus RNA-seq of frozen brain | 639 | Request, Synapse |
Proteomics
| Type | Description | Sample Size | More Info / Request Data |
|---|---|---|---|
| Proteomics SRM | Selected reaction monitoring proteomics | 1225 | Documentation, Request, Synapse |
| Proteomics TMT | Tandem mass tag proteomics | 946 | Documentation, Request, Synapse |
| Proteomics ELISA | Presynaptic proteins and SNARE protein-protein interactions | 554 | Documentation, Request |
| Proteomics Somalogic | Plasma proteomics | 671 | Request |
Metabolomics
| Type | Description | Sample Size | More Info / Request Data |
|---|---|---|---|
| Bile acid | Selected bile acid concentration in brain tissue | 111 | Documentation, Request, Synapse |
| Brain metabolomics | Selected metabolites quantification in brain tissue | 111 | Documentation, Request, Synapse |
| Serum metabolomics | Selected metabolites quantification in serum | 603 | Documentation, Request, Synapse |
| Brain lipidomics | Targeted LC-MS measurements of 123 lipids in brain tissue | 99 | Documentation, Request |
| Serum lipidomics | Targeted LC-MS measurements of 33 lipids in serum | 200 | Documentation, Request |
| Brain metabolomics Metabolon | Metabolites quantification in brain tissue (Metabolon) | 514 | Synapse |
| Brain lipidomics | LC-MS measurements of lipids in brain tissue | 384 | Synapse |