PIPELINE Core

The PIPELINE Core advances precision environmental health research by providing access to “omic” expertise and technologies.

The PIPELINE (Promoting Impact on Precision EHS by Leveraging Instrumentation, NextGen and Emerging Technologies) Facility Core encompasses world-class expertise and resources in state-of-the-art imaging with continually evolving genomic, epigenomic, metabolic and proteomic, and informatics approaches, applied from the single-cell to population level studies.

The overall goal of the PIPELINE Facility Core is to advance precision environmental health research by providing access to expertise and technologies and facilitating effective utilization of “omic” technologies across the parent organizations of the GC-CPEH. “Omics” data and integrative bioinformatics meet the research needs of Center Members to achieve systems level insights.

PIPELINE Leadership

Dr. Chris Amos, Director

Christopher Amos, Ph.D., Director
Baylor College of Medicine

Aaron Thrift, Ph.D. Career Development Leader-in Training
Baylor College of Medicine

Dr. Cristian Coarfa, Co-Director

Cristian Coarfa, Ph.D., Co-Director
Baylor College of Medicine

PIPELINE Resources

The PIPELINE Core leverages well established resources that exist across the TMC and parent organizations of the GC-CPEH to bring NextGen technologies to members.

CellOmics: Integrated Microscopy Core

Navigator: Dr. Michael Mancini, Baylor College of Medicine

  • Light microscopy
  • Super-resolution microscopy (SIM and STORM)
  • Live imaging (ultrafast and long-term)-Multi-dimensional spatial analysis
  • High throughput microscopy
  • Image analytics

Genomic and RNA Profiling

Navigator: Dr. Daniel Kraushaar, Baylor College of Medicine

  • Sample Quality Control
  • NGS
    • RNA-Seq
    • ChIP-Seq
    • Whole genome sequencing
    • Whole genome bisulfite sequencing
    • Targeted Sequencing
    • Sequencing only
  • NanoString Gene Expression Assays

Mass Spectrometry Proteomics

Navigator: Dr. Anna Malovannaya, Baylor College of Medicine

  • Consultation and Project design
  • 365 Proteome Profiling
  • Protein Complex Identification and Affinity Proteomics
  • Post-Translational Modification (PTM) Analysis
  •  “Per-Band” Sequencing
  • Data Analysis

Metabolomics

Navigator: Dr. Nagireddi Putluri, Baylor College of Medicine

  • Sample Preparation and Quality Control
  • Targeted Steady-State Analysis
  • Unbiased Steady-State Metabolomics
  • Lipidomics
  • Metabolomic Flux Analysis

Microbiome and Metagenomics

Navigator: Dr. Kristi Hoffman, Baylor College of Medicine

  • DNA and RNA Extraction
  • Targeted Amplicon Sequencing
  • Untargeted Virome Amplicon Sequencing Metagenome and Complete Genome Sequencing
  • Qualitative PCR
  • Data Analysis

Mouse Metabolism and Phenotyping

Navigator: Dr. Christopher Ward, Baylor College of Medicine

MultiOmics Data Analysis

Navigator: Dr. Cristian Coarfa, Baylor College of Medicine

  • Consultation
  • Primary Analysis of Data by Different Tech Platforms
  • Integrative MultiOmics Analysis
  • Data Deposition

Protein and Monoclonal Antibody Production

Navigator: Kurt Christensen, Baylor College of Medicine

  • Monoclonal Antibody Production
  • Protein Expression and Purification
  • Peptide Synthesis (3rd-party fee-for-service)
  • Biochemical Assays (3rd-party fee-for-service)

Single Cell Genomics

Navigator: Dr. Rui Chen, Baylor College of Medicine

  • Single Cell RNA Profiling
  • Single Cell ATAC-seq
  • Smartseq RNA profiling

UTHealth Human Genetics Center

Navigator: Dr. Alanna Morrison, UTHealth Houston

  • Genomics
    • Whole genome, whole exome
  • Epigenomics
    • Whole genome, RRBS, Capture
    • ChIP-Seq
  • Transcriptomics
  • Single Cell Genomics
    • RNA-Seq, ATAC-Seq

UTMB Inhalation Toxicology Core

Navigator: Dr. Bill Ameredes, UTMB Galveston

  • Inhalation/Exposure Laboratories
  • Cigarette Smoking/Inhalation
  • Airway/Lung Physiology Laboratories
  • ITC Facility Brochure

UTMB Mass Spectrometry Proteomics

Navigator: Dr. Bill Russell, UTMB Galveston

  • Intact molecular weight measurement
  • Protein identification from gel bands
  • Protein identification from complex mixtures
  • Identification of post-translational modifications
  • SILAC, iTRAQ, and label-free quantification of peptides and proteins
  • Small molecule quantification
  • Metabolomics

UTMB Next Generation Sequencing

Navigator: Dr. Steven Widen, UTMB Galveston

  • ChIP-Seq
  • De novo assembly
  • Variant identification
  • SNPs
  • Transcriptome (reference-guided or de novo)
  • miRNA and small ncRNA sequencing
  • Quantitative – RNA-Seq expression analysis
  • Exome Sequencing (Cancer or Custom Panels)

Request PIPELINE Services

The PIPELINE Core serves members with support at all stages of a project, including overall design, execution, data acquisition, and data integration and interpretation. Please submit the GC-CPEH Facility Core Service Request Form to begin your request.

Any Questions?

Contact Dr. Heyreoun An Han for more information.