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Methods and instruments that enable human genetic and genomics research

Boston

Service Description

Epidemiology and Genetics Core

Providing a central focus to translate the findings from clinical and cellular studies to applications in ongoing epidemiologic studies. This includes:

  • Providing access to large longitudinal datasets at Harvard for potential collaborations and meta-analyses. The cohorts include the NHS, NHS II, NHS 3, HPFS, GUTS, Framingham, Project Viva, and several national datasets. Detailed and repeated measures of diet, lifestyle, BMI, waist/hip circumference, weight change have been collected in these cohorts.
  • Providing efficient access and liaison with the Harvard Partner Genotyping Facility for high-throughput genotyping of clinical and epidemiologic samples in obesity-related studies.
  • Collaborating with investigators for the purpose of testing and replicating novel genetic associations of obesity and its related phenotypes in large nested case-control studies using readily available DNA samples through whole genome amplification.
  • Provide existing genotype data from the cohort studies for the purpose of pooling analyses or meta-analyses, in silico replications, and looking up SNPs from functional and experimental studies.

Have Questions? Contact Us.

Frank B. Hu, MD, PhD, Director
Email • Phone: (617) 432-0113

 

 

Service Description

Functional Genomics and Bioinformatics Core

Provides services to investigators looking to expand their research using state-of-the-art genomic applications. It utilizes next generation technologies and sequencing platforms to help identify the complex molecular mechanisms underlying human disease. Core staff can consult with researchers to ensure optimal experimental design on a case-by-case basis. Downstream or stand-alone data analysis pipelines are also offered to help researchers get the most from their datasets.

  • Consultation regarding experimental design and cost analysis
  • Sample quality assessment of DNA and RNA using the BioAnalyzer and Qubit assays
  • Next-generation sequencing library construction from RNA and DNA, including ChIP-Seq, ATAC-Seq, and MeDIP-Seq
  • Stand-alone sequencing services using the NextSeq 500 System
  • Basic data analysis, such as quality assessment and normalization, genomic alignment, differential expression/enrichment, GSEA, sample clustering, and motif enrichment
  • Advance data analysis on a consultative basis to maximize dataset potential

Have Questions? Contact Us.

Evan D. Rosen, MD, PhD, Director
Email • (617) 735-3222

Harvard Medical School

Service Description

Genomics and Cell Biology Core

Facilitating the application of cutting-edge genomics, bioinformatics, cell biology, and immunology techniques to nutrition and metabolic research. Services include:

  • Individual training concerning strategic design of next-generation sequencing, nanoString, and microarray-based transcriptional profiling, and other genomics-related experiments
  • Individual training concerning bioinformatic analysis of next-generation sequencing, nanoString, microarray, proteomics, and other genomics-related data sets
  • Construction of next-generation sequencing libraries from submitted DNA or RNA
  • Next-generation sequencing using the Illumina platform and other technologies as appropriate, with a major focus on RNA-Seq, metagenomics, ChIP-Seq, and other experimental applications
  • Choice of representative genes for nanoString transcriptional profiling analysis and nanoString analysis using the nanoString Preparation Station and “nCounter” Digital Analyzer

Have Questions? Contact Us.

Frederick M. Ausubel, PhD, Director
Email • (617) 726-5969

 

Service Description

Metabolic Phenotyping Core

Providing users with access to high-quality model creation and detailed metabolic phenotyping. Services include:

  • Immortalized cells, primary adipocytes or hepatocytes
  • Compound, drug, or metabolite-treated
  • siRNA or shRNA-mediated gene knockdown
  • CRISPR-mediated gene knockout
  • CRISPR-mediated sequence specific alteration
  • Overexpression of genes of interest

Have Questions? Contact Us.

Susan Newman, Co-Director
Email •Phone: (225) 763-0255

Richard Carmouche, Co-Director
Email •Phone: (225) 763-0257

Mid-Atlantic, Maryland

Service Description

Biological Mechanisms and Functional Genomics Core

Provides services to assist investigators in understanding biological, cellular and molecular mechanisms to address nutrition and obesity related problems.

Consultation and Training

  • Consultation in design of experimental approaches and training in specialized methods of adipose biology

Tissue/Cell Characterization and Repository

  • Access to fresh and frozen human samples from multiple tissue types, including fat tissue and skeletal muscle.

Analytical and Biological Assays

  • Assays: acute secretion, lipolysis, glycerol assay, fat cell size, LPL, HSL, protein, triglyceride, and cholesterol, NEFA, cellular lipids, TLC, in vitro radioisotopes tracer studies (lipogenesis, triglyceride synthesis, lipolysis)

Functional Genetic and Protein Assessment In Vivo and In Vitro

  • Gene and protein expression: Plasmid isolation, DNA &RNA isolation, cDNA and RT-PCR, Luminex and gene chip, molecular cloning, bacterial expression, western blot, activity assay
  • Imaging: Confocal use (time-lapse, FRET, FRAP), histocytochemistry
  • Adenovirus: Molecular cloning, viral vector construct, virus generation, amplification and purification

Zebrafish Models

  • Transient gene knockdown and embryonic/larval phenotyping, in vivo variant functional testing, genomic gene knockout (CRISPR), whole mount gene expression analysis, tissue specific gene expression analysis, protein expression analysis, whole mount lipid analysis (oil red o), total cholesterol and LDL-c quantification, vascular lipid accumulation analysis, tissue-specific phenotyping using transgenic lines (pancreatic beta-cells, exocrine pancreas, liver, neuronal tissues), dietary manipulation (high fat diet, high cholesterol diet), food intake quantification, dietary lipid metabolism assays

Have Questions? Contact Us.

Carole Sztalryd Woodle, PhD, Director
Email • Phone: (410) 706-4047

New York

Molecular Biology and Molecular Genetics Core

Service Description

Applying the tools and technologies of molecular genetics and genomics to elucidate the molecular-genetic bases of obesity and its comorbidities.

  • DNA Extraction (from mouse tail, from blood)
  • RNA Isolation (mouse analysis, human analysis)
  • Copy Number (affy array)
  • RNAseq
  • Exome Sequence (mouse analysis, human analysis)
  • Low Density Arrays
  • CHiP Analysis
  • Modifications (methylation analysis, histone modification analysis)
  • Single Cell RNAseq Analysis
  • Mice (Ob on BALB/cJ, ob with Agrp-/-, db on C57BL/6J, lepr-floz on FVB/NJ, lepr-floz with NPY-/- on FVB/NJ)
  • Transgenic Mice (design of mouse, injection into hybrid cell)
  • Bioinformatics Analysis
  • iPSC Generation (skin biopsy, fibroblast differentiation, iPSC generation)
  • iPSC Differentiation (differentiation into beta cells, differentiation into hypothalamic cells)
  • CRISPR (primer design)

Have Questions? Contact Us.

Wendy Chung, MD, PhD, Director
Email • Phone: (212) 851-5313

Pennington Biomedical Research Center

Service Description

Molecular Mechanisms Core

Next-Generation sequencing of 16s V3/V4 or V4 regions.

Have Questions? Contact Us.

Susan Newman, Co-Director
Email •Phone: (225) 763-0255

Richard Carmouche, Co-Director
Email •Phone: (225) 763-0257

 

 

 

Service Description

Molecular Mechanisms Core

Literature search for gene sets in 18 biological dimensions including pathways, diseases, chemicals/drugs, cell lines, metabolism and cell biology.

Have Questions? Contact Us.

Susan Newman, Co-Director
Email •Phone: (225) 763-0255

Richard Carmouche, Co-Director
Email •Phone: (225) 763-0257

 

 

 

 

Service Description

Molecular Mechanisms Core

Next-Generation sequencing to detect protein binding sites.

Have Questions? Contact Us.

Susan Newman, Co-Director
Email •Phone: (225) 763-0255

Richard Carmouche, Co-Director
Email •Phone: (225) 763-0257

 

 

 

Service Description

Molecular Mechanisms Core

Analysis of human gene expression microrarrays using the Illumina-Human HT-12.

Have Questions? Contact Us.

Susan Newman, Co-Director
Email •Phone: (225) 763-0255

Richard Carmouche, Co-Director
Email •Phone: (225) 763-0257

 

 

Service Description

Molecular Mechanisms Core

Next-Generation sequencing to detect whole RNA.

Have Questions? Contact Us.

Susan Newman, Co-Director
Email •Phone: (225) 763-0255

Richard Carmouche, Co-Director
Email •Phone: (225) 763-0257

 

 

 

 

Service Description

Molecular Mechanisms Core

Robotic pipetting services for 384 well qPCR plates.

Have Questions? Contact Us.

Susan Newman, Co-Director
Email •Phone: (225) 763-0255

Richard Carmouche, Co-Director
Email •Phone: (225) 763-0257

 

 

 

 

Service Description

Molecular Mechanisms Core

Next-Generation Sequencing to detect global gene expression.

Have Questions? Contact Us.

Susan Newman, Co-Director
Email •Phone: (225) 763-0255

Richard Carmouche, Co-Director
Email •Phone: (225) 763-0257

 

 

 

 

Service Description

Molecular Mechanisms Core

Next-Generation sequencing to detect small RNA including miRNA.

Have Questions? Contact Us.

Susan Newman, Co-Director
Email •Phone: (225) 763-0255

Richard Carmouche, Co-Director
Email •Phone: (225) 763-0257

 

 

Service Description

Molecular Mechanisms Core

Sequencing of Plasmid DNA or PCR fragments using capillary electrophoresis.

Have Questions? Contact Us.

Susan Newman, Co-Director
Email •Phone: (225) 763-0255

Richard Carmouche, Co-Director
Email •Phone: (225) 763-0257

University of California, San Francisco

Service Description

Genetics and Genomics Core

Providing an array of sophisticated methods and instruments that enable human genetic and genomics research and/or the tools to generate genetic models to test hypotheses.

Genomics Services

  • Provides key services for genetic and genomic research, including DNA extraction, SNP genotyping, gene expression, DNA and RNA sequencing, and data analysis/storage.

Viracore

  • Provides information, training, assistance and resources for experiments to be performed by individual investigators by providing: 1) Essential reagents, equipment, training, supervision, and monitoring of investigators wishing to ensure the proper compliance with biosafety containment required for lentiviral-based research. 2) Lentiviral preparation services for investigators. 3) Education on RNAi experimentation, through the lentiviral core website, and through protocols available at the facility.

Gene Targeting

  • Provides high-quality ES cell services with a high probability of germline transmission. The core offers ES cell targeting, genomic DNA extraction from 96-well plates, expansion of targeted ES cells, chromosome counts, and preparation of ES cells for microinjection.

Transgenics

  • Transgenic and knockout technologies enable investigators to learn how specific genes and proteins, or their variants, function in a natural living animal environment with a defined genetic background in ways not possible by other experimental approaches. At the Gladstone Institutes transgenic mouse models have been used to understand how specific genes affect atherosclerosis, Alzheimer’s disease, obesity, AIDS, and other diseases and disorders that impact modern life
  • Provides services including microinjection of DNA for producing transgenic mice, microinjection of ES cells for producing gene knock-out mice, and 8 cell microinjection for producing 100% ES cell derived mouse embryos or mice.

Cryopreservation and Resuscitation

  • Provide services including sperm and embryo cryopreservation; sperm and embryo resuscitation; and expansion by in vitro fertilization.

Rederivation

  • The rederivation procedure by which an early, pre-implantation stage embryo is isolated from the reproductive tract of one mouse (donor female) and transferred to the reproductive tract of a mouse (recipient female) made pseudopregnant in order to allow implantation, gestation, and birth. The rederivation procedure consists of collection, in vitro maturation and embryo transplantation.

Have Questions? Contact Us.

Jeremy Reiter, MD, PhD, Director
Email •Phone: (415) 502-8528