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Functional Genomics

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Theo Bammler photo Theo Bammler, Ph.D., Coordinator, tbammler@uw.edu Lu Wang Lu Wang Jim MacDonald Jim MacDonald  

The Interdisciplinary Center for Exposures, Diseases, Genomics & Environment (EDGE)

The Functional Genomics Component focuses on the biochemical and molecular mechanisms underlying human variability, and fosters collaborations between a large network of investigators working in toxicology, molecular biology, genetics, and environmental epidemiology. Technical support is provided through five facility cores, one of which is the Functional Genomics Component that addresses IDD research for our Genetics Core.

Functional Genomics Laboratory Services include:

UW Interdisciplinary Center for Exposures, Diseases, Genomics & Environment (EDGE) - Direct & Linked)

EDGE Bioinformatics and Biostatistics Unit (BBU - Direct)
BBU Office: The IDDRC Functional Genomics Component staff occupy 150 sq ft of office and 100 sq ft of computer training laboratory within EDGE, adjacent to wet laboratory space. This space contains dedicated workstations and the statistical and bioinformatics software packages necessary for the proposed analysis.

Computer hardware and software used by the BBU for statistical and bioinformatics analysis: 4 Dell Precision T3500 Windows workstations, a Dell Precision T3600 Windows workstation, a Dell Precision T1700 Windows workstation, a storage server running Ubuntu Linux with dual Xeon E5620 CPU, 24 Gb RAM, and an 8 Tb direct-attached storage (DAS) in RAID10 configuration, as well as a high-end compute server running Ubuntu Linux with quad Xeon E5-4620 CPU (32 physical cores, 64 with hyperthreading), 256 Gb RAM, and a 29 Tb DAS in RAID10 configuration. In addition, the BBU also uses a high performance computing cluster, consisting of 8 nodes, over 200 cores, and 3TB of RAM. The system is configured to support additional expansion as needs change. Nodes consist of dual Xeon 5118 (12-cores each), 384GB RAM, and 200GB of high speed local scratch space. Cluster nodes are interconnected using dual-path 10Gb ethernet for performance and reliability. The cluster is configured to support both batch and interactive workloads, ranging from single-core to multi-node. All cluster nodes are running the Rocks 7 Linux Distribution.
The BBU has a suite of both commercial and Open Source bioinformatics and statistical software for data analysis. The bulk of most types of analyses is performed in the R statistical environment (www.r-project.org), using various packages from the Bioconductor project (www.bioconductor.org). The Bioconductor project supplies both cutting-edge software for the analysis of OMICs data as well as various SQLite-based annotation packages that allow integration of results with gene, transcript, or protein based information. Of note are the minfi, DMRcate, edgeR and bumphunter packages. In addition, the BBU has a license for iPathwayGuide Analysis (https://advaitabio.com), a commercial software tool that uses data mined from public sources as well as proprietary data to infer networks or pathways that are perturbed in a given experiment. Other more specific software include MACS or csaw for ChIP-Seq, the tuxedo suite (Bowtie/Bowtie2, Tophat, Cufflinks), subread, gmap/gsnap, salmon, and kallisto for aligning RNA-Seq data, Bismark for BS-Seq, Fastqc, Fastx, seqtk, samtools, cutadapt, and Picard for quality control and manipulation of FASTQ and sam/bam file formats, Trinity, Trinotate and a local install of NCBI BLAST for de novo transcriptome generation and annotation, and bedtools, bedops, and the UCSC toolset for working with gff, bed, wig, bigwig, and 2bit file formats.  Other R packages for metabolomics and proteomic data anlysis include limma, MSstats, impute, and NormalizeMets. For microbiome 16S sequence analysis, R packages include DADA2, phyloseq, vegan,metageomeSeq, and other microbiome functional analysis tool such as PICRUSt2, BURRITO and FishTaco.

EDGE Functional Genomics, Proteomics and Metabolomics Facility (FGPM - Linked)

FGPM Office: The FGPM staff occupies an office of approximately 100 sq ft, in close proximity to the wet laboratory space. Within the laboratories, several desk areas are provided for laboratory personnel. Both the offices and laboratory areas contain desktops that provide computer resources and email access.

FGPM Laboratory: The FGPM occupies approximately 1500 sq ft of laboratory space (in three adjoining rooms). This laboratory has ready access to common lab facilities including a cold room, a warm room, general common equipment room, and a tissue culture facility. These labs contain standard facilities including two 6 ft fume hoods, stainless steel sinks, lab benches, three -20°C freezers, four -80°C freezers, three 4°C refrigerators; 6 Fisher MicroV microcentrifuges, 2 Spectrafuge 16M microcentrifuges, Hermle Z230MR and MR-2 microcentrifuges, two Savant integrated speedvac systems, two Beckman GS-15R centrifuges with fixed (F2402) and swinging (S4180, S2096) bucket rotors, one Heraeus Multifuge 3S+ Centrifuge, one Eppendorf 5804 Centrifuge, 4 Eppendorf Mastercycler thermal cyclers, 4 ABI 2720 thermal cyclers, two MJ Research PTC-200 DNA Engine single block thermal cyclers, MJ Research PTC-225 DNA Engine Tetrad four block thermal cycler, four ABI/PE GeneAmp 9700 thermal cyclers, two Bio-Rad Gel Doc 1000 electrophoresis gel documentation systems, an Applied Biosystems™ QuantStudio™ 7 Flex Real-Time PCR System, BioMark HD System by Fluidigm, Beckman DU 650 spectrophotometer, Spectra Max Plus and 190 high throughput spectrophotometers, Packard ScanArray 5000XL Microarray Scanner, a GenePix 4000B DNA Microarray Scanner (Axon Instruments, Inc), an Affymetrix GCS3000 Scanner with autoloader, an Affymetrix GeneChip Node system for processing Affymetrix GeneChip microarrays and custom GeneChip ParAllele TrueTagTM arrays, an Agilent DNA microarray scanner and hybridization oven for processing Agilent arrays, an Agilent 2100 Bioanalyzer, a DNA microarray hybridization oven and related equipment for processing other types of microarrays, NanoDrop ND-1000 Spectrophotometer, two HS 400 Pro Automated Hybridization/Wash Stations (Tecan U.S., Research Triangle Park, NC) with quad heads. A PyroMark Q24 platform (Qiagen Inc., Valencia, CA) is available allowing quantitative epigenetic methylation measurement at single base-pair resolution. The FGPM addresses quantitative analysis of specific proteins using ELISA, a Luminex System, a MagPix system, or a Meso Quick Plex SQ 120 system from Meso Scale Discovery. For NextGen sequencing applications (e.g., RNA-Seq, ChIP-seq, bisulfite sequencing), an Illumina HiSeq 4000 and NovaSeq platform are available through the UW Northwest Genomics Center (http://nwgc.gs.washington.edu/). For methylation profiling of human samples using the Illumina Infinium MethylationEpic bead array platform, an Illumina Infinium Methylation EPIC 8-Sample Beadchip, and an Illumina iScan+ with ICS v3.3.28, as well as the Illumina GenomeStudio software (GenomeStudio v2011.1 with Methylation Analysis Module v1.9.0) are available at the Genomics Shared Resource (GSR) at the Fred Hutchinson Cancer Research Center (FHCRC).

Computer hardware and software associated with sample processing: 13 Macintosh computers: 6 iMac 5.1 (Intel Core 2 Duo, 2.16 GHz) computers, and 7 Power Macintosh G4s. The Lab has many software programs designed for molecular biology-based research including EuGeneTM (Daniben Systems, Cincinnati, OH), SequencherTM 3.0 (Gene Codes Corp, Ann Arbor, MI), GeneScanTM, PrimerExpressTM (ABI, Foster City, CA) and Molecular AnalystTM (Bio-Rad Laboratories, Hercules, CA).  Computers that are associated with DNA microarray-based instrumentation: 1 HP Vectra (for Agilent 2100 Bioanalyzer), Dell Optiplex 280 (for Affymetirx microarray SNP chips), Dell Precision 330 (for GenePix 4000B Microarray Scanner), Optiplex GX240 (for Packard ScanArray 5000XL Microarray Scanner), Dell Optiplex 755 (for Nanoquant spectrophotometer), and two Dell Precision 670 Workstations (Affymetrix microarray scanner computers).

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University of Washington • Center on Human Development and Disability Box 357920 • Seattle WA 98195-7920 USA • 206-543-7701 • chdd@uw.edu