Technologies
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10X Genomics: 10x Genomics' single cell sequencing technology is based on microfluidic technology and enables high-throughput, high-precision single cell analysis.
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Parse Biosciences: Plate-based combinatorial barcoding for high-throughput single-cell sequencing; supports fixation/batching and requires no instrument.
Instrumentation
- Single-cell genomics:
- 10X Genomics - Chromium X: Automated single-cell/nuclei partitioning and barcoding for high-throughput scRNA-seq, ATAC-seq, and multi-omics.
- Spatial transcriptomics:
o 10X Genomics - Visium CytAssist: Sequencing-based spatial transcriptomics. Uses
probe-based chemistry to provide whole transcriptome analysis with spatial context.
o 10X Genomics - Xenium Analyzer: Imaging-based spatial transcriptomics employs
padlock probes to selectively target pre-selected genes. This approach provides a
nanometer-scale resolution, enabling the analysis of up to 5,000 genes within individual
cells across entire tissue sections.
Automation
o Integra Assist Plus: A semi-automated pipetting platform that standardizes small
to medium workflows utilizing electronic pipettes, particularly suited for NGS library
preparation, including Parse single-cell library preparation.
Cell processing & Cell sorting
o Miltenyi gentleMACS: Standardized mechanical dissociation of tissues into single
cells or nuclei.
o Miltenyi autoMACS® Neo: Automated magnetic cell separation for positive/negative
selection.
o Miltenyi MACSQuant® Analyzer: Flow cytometer for multiparameter immunophenotyping
and cell counting.
o Miltenyi MACSQuant® Tyto: Closed, sterile microchip-based cell sorter for gentle,
contamination-free enrichment.
Histology & Tissue Handling:
o Nikon Eclipse Ti2 Microscope: Inverted research microscope for imaging, QC, and
live-cell/tissue observations.
o Epredia™ HM 355S Automatic Microtome: High-precision paraffin sectioning for consistent
tissue ribbons.
o Epredia™ Section Transfer System (STS): Automated warm-water transfer of sections
from microtome to slides.
o Epredia™ Digital Round Tissue Section Waterbath: Flattens and relaxes paraffin
sections before mounting.
o Epredia™ High-Capacity Section Dryer: Rapid drying and adhesion of slides prior
to downstream staining or imaging.
The core can also handle bioinformatics analysis downstream of the experimental workflows described above
- SERVICES PROVIDED
10X Genomics - Chromium X
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GEM-X Universal 3' Gene Expression
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GEM-X Universal 5' Gene Expression
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GEM-X Flex Gene Expression
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Next GEM Flex Gene Expression
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Next GEM Epi ATAC
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Next GEM Epi Multiome
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Next GEM Universal 3' Gene Expression (including HT)
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Next GEM Universal 5' Gene Expression (including HT)
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10x Genomics – Visium Cytassist
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HD WT Panel Gene Expression
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HD 3’ Gene Expression
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10X Genomics – Xenium
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Xenium Ready-to-use panels are compatible with human, mouse, and additional species with custom panels. Compatible samples include FFPE tissue, fresh-frozen tissue, and tissue microarray (TMA).
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Parse Biosciences
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Parse Evercode Whole Transcriptome assay, Parse Evercode kits are currently available in four sizes, allowing for the capture of approximately 10,000, 100,000, 1,000,000, or 5,000,000 total cells or nuclei from up to 12, 48, 96, or 384 samples, respectively.
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PERSONNEL
Professor Yehia Mechref -- CBG Director, Paul W. Horn Distinguished Professor, Robert A. Welch Chair in Chemistry and Associate Vice President of Research & Innovation. Email
Dr. Mohamed Fokar -- Scientific Coordinator, Genomics Core, Research Professor Center for Biotechnology and Genomics. Email
Dr. Isabel Castro-Piedras--Single Cell Genomics Core Manager, Assistant Professor of Practice, Center for Bioinformatics and Genomics. Email
Dr. Timothy Jobe -- Research Associate, Center for Bioinformatics and Genomics. Email
Dr. Chiquito J. Crasto -- Bioinformatics Core Manager, Research Professor, Center for Biotechnology and Genomics. Email
FUNDING
We gratefully acknowledge the funding provided by the Cancer Prevention and Research Institute of Texas (CPRIT)
Grant ID: RP250651
Title: Establishment of a Single-Cell Genomics Core Facility at Texas Tech University: Advancing Precision Cancer Research through Cutting-Edge Technologies
PI: Professor Yehia Mechref
Center for Biotechnology & Genomics
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Address
Texas Tech University, Canton & Main Experimental Sciences Building, Room 101, Lubbock, TX 79409, Mail Stop 3132 -
Phone
806.742.6927 | Fax: 806.742.3788 -
Email
chiquito.crasto@ttu.edu