VUMC Immunogenomics, Microbial Genetics and Single Cell Technologies (IMGSCT) core provides high throughput high resolution immunogenomics sequencing, including HLA typing, KIR typing, and ERAP typing. Additionally, the core will provide single-cell studies focused on TCR sequencing and RNA transcriptomics, microbial genetics assays and digital droplet PCR assays.
The Core provides support for:
The facility has pre and post PCR laboratories (rooms U3304 and U3308) that contains two Biomek Robotic liquid handling systems for automated, high throughput assays . Liquid handlers are used wherever possible in order to minimize manual handling of samples. IMGSCT core also has a Mantis which is a microfluidic liquid handling device, useful when working with very small volume reactions. The Mantis enables us to reduce reagent cost which in turn help us having competitive pricing for single cell assays.
The IMGCT Core also has Droplet Digital instrument, PCR and, Realtime PCR instruments.
Droplet Digital™ PCR (ddPCR™) is an elegant technology that enables accurate and absolute quantification of target nucleic acid molecules. By partitioning a PCR reaction into thousands of nanoliter-sized droplets followed by amplification and subsequent interrogation of each droplet, ddPCR assays allow increased quantitative resolution, enhanced detection of difficult-to-amplify targets, better reproducibility, and simplified data analysis.
Description of services
We ship samples to the Institute for Immunology and Infectious Diseases (IIID) in Perth, Australia for our collaborators to process. Our core was built and designed to mirror this high throughput laboratory that was partly designed by members in our group. They have automated systems, with large throughput work flow and standard operating procedures that facilitate the generation of large volume work-loads from all over the world in an expedited manner. IIID is accredited by the National Association of Testing Authorities, Australia and American Society for Histocompatibility and Immunogenetics(ASHI) for compliance to the ISO/IEC 17025 standard for laboratory testing and HLA typing respectively(http://www.iiid.com.au). Final analyzed results are sent to Investigators through IMGSCT core.
Using the smart seq 2 technology we generate cDNA from sorted single cells, amplifying TCR from barcoded cDNA from each cell and sequenced on Illumina Mi Seq platform (IIID)
Single cell whole libraries are made from sorted single cells individually barcoded (IMGCT) and sequencing is done at VANTAGE core on Novaseq
Bulk TCR sequencing of bulk T cell populations(lysates or RNA), Viral and Bacterial genome sequencing is also performed at IIID, and analyzed data will be sent to the Investigators through IMGCT core.
Data analysis is via VGAS, with a 3-month access provided to users to analyze data with option of extension as needed
Simon Mallal, Core Scientific Director
Elizabeth Phillips, Core Scientific Co-Director
Suman Das, Core Deputy Director
Rama Gangula, Core Operations Manager
For general questions or assistance, please contact our support team at IMGSCTCore@vumc.org
Hours | Location |
Monday-Friday, 8:00am-4:30pm |
MCN U-3308 |
Services & Rates |
► Analysis (2) | |||
Name | Description | Price | |
---|---|---|---|
Bioinformatics per hour | Inquire | ||
Biostatistical Immunogenetics per hour | Inquire | ||
► Genome Sequencing (3) | |||
Name | Description | Price | |
Bacterial Genome Sequencing per sample |
Pricing Subject to Change based on project requirements |
Inquire | |
HIV-Viral Genome Sequencing>24 per sample | Inquire | ||
HIV-Viral Genome Sequencing<24 per sample | Inquire | ||
► Genotyping (14) | |||
Name | Description | Price | |
ERAP Typing >48 per sample | Inquire | ||
ERAP Typing <48 per sample | Inquire | ||
HLA Typing >999 (Per Sample) | Inquire | ||
HLA Typing <10 (per sample) | Inquire | ||
HLA Typing + KIR Allele Genotyping >48 (per sample) | Inquire | ||
HLA Typing + KIR Allele Genotyping + ERAP Typing >48 (per sample) | Inquire | ||
HLA Typing 10 -48 (Per Sample) | Inquire | ||
HLA Typing 49 - 999 (Per Sample) | Inquire | ||
KIR Allele Genotyping >999 (per sample) | Inquire | ||
KIR Allele Genotyping <10 (Per sample) | Inquire | ||
KIR Allele Genotyping 10 - 48 (per sample) | Inquire | ||
KIR Allele Genotyping 49 - 999 (per sample) | Inquire | ||
KIR Typing >48 (Per sample) | Inquire | ||
KIR Typing <48 (per sample) | Inquire | ||
► Nucleic Acid Extraction (1) | |||
Name | Description | Price | |
DNA Extractions per sample - Only for HLA related requests | Inquire | ||
► Nucleic Acid Quantitation (1) | |||
Name | Description | Price | |
ddPCR per sample |
Full-Service |
Inquire | |
► Single cell Technologies (13) | |||
Name | Description | Price | |
Addition of Cite-seq Ab cost per sample | Inquire | ||
Addition of Hashtag per sample | Inquire | ||
Bulk TCR Sequencing from RNA>12 per sample | Inquire | ||
Bulk TCR Sequencing from RNA<12 per sample | Inquire | ||
Cite seq staining for 10X per sample | Inquire | ||
Single Cell 3'RNA seq <24pl(not Including cDNA conversion) per plate | Inquire | ||
Single Cell 3'RNA seq>24pl(not including cDNA conversion) per plate | Inquire | ||
Single Cell cDNA and TCR Seq per plate | Inquire | ||
Single Cell cDNA-384 well plate (Per Plate) | Inquire | ||
Single Cell cDNA-96 well plate (Per Plate) | Inquire | ||
Single Cell Whole Transcriptome Seq per plate (cDNA provided) | Inquire | ||
Single Cell Whole Transcriptome Seq per plate (including cDNA conversion) | Inquire | ||
TCR Sequencing Only per plate | Inquire |