Pipeline Facility Core
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 Facility Core Leadership
Director
Baylor College of Medicine
Co-Director
Baylor College of Medicine
Leadership Development Program Participant (LDP)
Baylor College of Medicine
PIPELINE Facility Core Resources
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.
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: Dr. Dean Edwards, 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 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
- Integration with UTMB Imaging Network for lung and eye toxic responses; fixed and live-cell imaging; microCT-PET-SPEC, molecular optical imaging (IVIS) and Optical Coherence Tomography (OCT)
- 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)
UTMB Center for Single-Cell Genomics
Navigator: 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
Request PIPELINE Facility Core Services
GC-CPEH Full members and Pilot Project awardees utilizing the PIPELINE Facility Core Resources are eligible for the Center subsidies to underwrite their costs up to 25 to 50%.
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
gc-cpeh@bcm.edu
Cite the Center
Please remember to cite center in your publications.
“Research reported in this publication was supported by the National Institute of Environmental Health Sciences of the National Institutes of Health 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.”