Omics Overview

Example Projects using ROS-MAP Omics

plot of chunk twoWayStatsPlot Methylation Normalization

Molecular Networks Molecular Networks

Brain xQTL Serve 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.

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 1164 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 In Process
ATAC Seq Chromatin Conformation In Process

Gene Expression (mRNA)

Type Description Sample Size More Info / Request Data
RNAseq Next-generation RNA sequencing 638 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 615 Synapse
snRNAseq Single-nucleus RNA-seq of frozen brain 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 160 Documentation, Request, Synapse
Proteomics ELISA Presynaptic proteins and SNARE protein-protein interactions 554 Documentation, 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