Pipeline Facility Core
The PIPELINE (Promoting Impact on Precision EHS by Leveraging Instrumentation, NextGen, and Emerging Technologies) Facility Core provides top-tier expertise and resources in advanced imaging and genomics, epigenomics, metabolomics, proteomics, and informatics. It supports studies from single-cell to population level. The goal is to advance precision environmental health research to prevent disease and improve human health. PIPELINE FC offers specialized expertise prioritized access and facilitates the use of “omics” technologies, helping researchers across the Center’s Thematic Focus areas integrate these technologies into their research.
PIPELINE Facility Core Leadership
Director
Baylor College of Medicine
Co-Director
Baylor College of Medicine
Leadership Development Program Participant
Baylor College of Medicine
The PIPELINE Facility Core leverages well-established resources that exist across the TMC and parent organizations of the GC-CPEH to bring NextGen technologies to members. The PIPELINE Facility Core serves members with support at all stages of a project, including overall design, execution, data acquisition, and data integration and interpretation.
PIPELINE Facility Core Resources
BCM Genomic and RNA Profiling
Navigator: Dr. Daniel Kraushaar, Baylor College of Medicine
- Sample Quality Control; Next-Generation Sequencing: RNA-Seq, ChIP-Seq, Whole-Genome Sequencing, Whole-Genome Bisulfite Sequencing, Targeted Sequencing, Sequencing Only; NanoString Gene Expression Assays
UTMB Next Generation Sequencing
Navigator: Dr. Haiping Hao, 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)
UTHealth Human Genetics Center
Navigator: Dr. Alanna Morrison, UTHealth Houston
- Illumina Whole-Genome and Consortium Arrays; Custom Mid- to High-Plex Genotyping; Custom Low- to Mid-Plex Genotyping; Epigenetics: Methylation Analysis; Illumina Laboratory Best Practices and Quality Control; Genomic Data Analysis and Quality Control; Sample Handling and Storage
UTMB Center for Single-Cell Genomics
Navigators: Dr. Haiping Hao, Dr. Peter McCaffrey, UTMB Galveston
- 10X Genomics Chromium workflows:
- Single-cell gene expression on fixed and fresh tissues
- Single-cell epigenomics (ATAC)
- Single-cell multi-omics (gene expression + ATAC)
- 10X Visum and Xenium workflows:
- Single-cell spatial transcriptomics (via 10X Visium)
- Single-cell in-situ transcriptomics (via 10X Xenium)
- Learn More
BCM Single Cell Genomics
Navigators: Drs. Chenghang (Chuck) Zong, Mira Jeong, Baylor College of Medicine
- Single-Cell RNA Profiling; Single-Cell ATAC-seq; Smartseq RNA profiling
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
BCM Mass Spectrometry Proteomics
Navigator: Dr. Anna Malovannaya, Baylor College of Medicine
- Consultation and Project design; 365 Proteome Profiling; Protein Complex Identification by IP/MS; Post-Translational Modification (PTM) Analysis; “Per-Band” Sequencing; Data Analysis
Metabolomics
Navigators: Drs. Nagireddi Putluri, Abu Hena Mostafa Kamal, 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
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
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
Protein and Monoclonal Antibody Production
Navigator: Dr. Dean Edwards, Baylor College of Medicine
- Recombinant Protein Expression; Protein and MAb Purification; Hybridoma/Monoclonal Antibody Production; Peptide Synthesis (third-party fee-for-service); Biochemical Assays (third-party fee-for-service)
Mouse Metabolism and Phenotyping
Navigator: Dr. Christopher Ward, Baylor College of Medicine
- Imaging; Blood Serum/Plasma Analysis; Cardiopulmonary; Metabolism; Cellular Metabolism; Glucose Metabolism; Lipid Metabolism; Whole-Body Metabolism; Other Tests; Challenges; Surgical and Anesthesia
Zebrafish Core
Navigator: Dr. Daniel Gorelick, Baylor College of Medicine
- Ues zebrafish for chemical screens, genetic screens, and to investigate how chemical exposures affect embryonic development at the molecular, cellular, and genetic levels
- Learn more>
UTMB Inhalation Toxicology Core
Navigator: Dr. Bill Ameredes, UTMB Galveston
- Inhalation/Exposure Laboratories, including Gaseous and Aerosol Toxicants; Allergens; Topical Dermal and Ocular Exposures; Intravitreal and Systemic Exposures; Tobacco and e-Cigarette Smoking/Vaping Inhalation; Hazardous Chemical-Approved Exposure Facility; Airway/Lung Physiology Function Assessment; Ocular and Skin Response Assessment; Cell Culture Exposure Facilities;; Fixed and Live-Cell Imaging; microCT-PET-SPEC, Molecular Optical Imaging (IVIS) and Optical Coherence Tomography (OCT)
- ITC Facility Brochure
Request Core Services & Matching Funds
Full members and Pilot Project awardees of GC-CPEH who use the PIPELINE Facility Core Resources are eligible for Center subsidies to cover 25 to 50% of their costs. Click here to learn more about the service request and matching fund review and approval process.
Please submit the GC-CPEH Facility Core Service Request Form to begin your request.
Any Questions?
Contact Dr. Heyreoun An Han for more information.
OUR INSTITUTIONS
One Baylor Plaza, MS 229, Houston, TX 77030
Email: gc-cpeh@bcm.edu
Citation for Center Support
“Research reported in this publication was supported by the National Institute of Environmental Health Sciences under Award Number P30ES030285. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.”
