NYMC > Research > Core Facilities & Shared Resources > Genomics Lab

Genomics Lab

The Genomics Core Laboratory in the Department of Pathology is established to house both basic and translational genomics research, allow individual investigators access to state-of-the-art next-generation sequencing (NGS) technologies, conduct genomics experiments and bioinformatics analyses, and provide opportunities for education and training in genomics and bioinformatics.

Instruments:

The Genomics Core Laboratory hosts a variety of instruments for carrying out genomics research. These instruments include, but are not limited to:

Qubit 2.0 Fluorometer for flurometric quantification of DNA, RNA and protein
Bioanalyzer 2100 for quantification, size and purity assessment of DNA, RNA and protein
TapeStation 4200 for quantification, size and purity assessment of DNA, RNA and protein
BluePippin for DNA size selection/collection ranged from 100 bp to 50 kb with pulse-field
Stratagene Mx3005P for real-time quantitative PCR
SpectraMax Gemini XPS microplate reader for fluorescence intensity assays
Biomek FXp automated workstation for high-throughput liquid handling and workflow
MiSeq for single- or paired-end short-read sequencing ranged from 50 bp to 300 bp
NextSeq 550 for single- or paired-end short-read sequencing ranged from 50 bp to 150 bp

Please click the instrument name for the link to its official website for overview and/or introduction.

The Genomics Core Laboratory mainly uses the Illumina MiSeq and NextSeq two sequencing systems as the NGS platform. The specifications of MiSeq and NextSeq are demonstrated in the table below.

 Genomics Core Instruments

Services:

The Genomics Core Laboratory provides and supports a variety of NGS services and their following bioinformatics data analyses. Consultation before services is freely available and is strongly recommended.

The NGS services include:

  • Whole Genome Sequencing (WGS)
    • Whole Exome Sequencing (WES)
  • Target gene panel sequencing
  • Whole Transcriptome Sequencing (RNAseq)
    • Small RNA (or microRNA) sequencing
  • Metagenomics or metatranscriptomics sequencing of microbiome
    • sequencing with chromatin immunoprecipitation (ChIP-seq)
  • sequencing RNA-binding protein immunoprecipitation (RIP-seq)
  • other custom-designed sequencings

The bioinformatics services include:

  • de novo assembly of genome/transcriptome
  • alignment- and mapping-based analysis of genetic variants
  • differential expression analysis of genes/microRNAs
  • pathway and network analysis of genes
  • species detection & gene identification in microbiome study
  • others with custom’s instruction and/or request

Core Pricing:

Consultation for the total cost of planned service is thus strongly recommended. Since the bioinformatics services are free of charge, a courtesy from the Genomics Core Laboratory, the co-authorship in your publications is greatly appreciated.

NA1:E58extSeq 550      
Service   Internal  External
       
Mid-Output      
150 bp sequencing   $1297.00 $1362.00
(2x75 bp)      
        
Mid-Output       
300 bp sequencing $2090.00 $2195.00
(2x150 bp)       
       
High-Output       
150 bp sequencing   $3410.00 $3581.00
(2x75 bp)       
        
High-Output       
300 bp sequencing $5462.00 $5735.00
(2x150 bp)      
        
MiSeq      
Service   Internal External
        
V2, 50 bp sequencing       
(1x50 bp)   $980.00 $1029.00
        
V2, 500 bp sequencing       
(2x250 bp)   $1410.00 $1481.00
        
V3, 150 bp sequencing       
(2x75 bp)   $1088.00 $1142.00
        
V3, 600 bp sequencing       
(2x300 bp)   $1841.00 $1933.00
        
Library Prep       
Service   Internal  External
       
TruSeq mRNA       
(polyT purification)   $ 160.00 $ 192.00
        
TruSeq mRNA       
(RiboZero purification)   $ 275.00 $ 330.00
        
TruSeq small RNA   $ 300.00 $ 360.00
        
Nextera XT   $ 100.00 $ 120.00
        
Others       
Service   Internal  External
        
Bioanalyzer 2100       
(DNA or RNA, per sample)   $ 15.00 $ 20.00
        
TapStation 4200       
(DNA or RNA, per sample)   $ 12.00 $ 15.00
        
BluePippin       
(size selection, per sample)   $ 25.00 $ 30.00
        
Stratagene Mx3005p      
Real-time PCR   inquire  inquire
        
Spectramax Gemini XPS       
Fluorometer 96-well   inquire  inquire
        
Biomek FXp       
(automation system)   inquire  inquire

 

Service Request:

Genomics Core Laboratory is located at Basic Sciences Building Room 409 at Pathology Department. Investigators are welcome to visit, consult, and request services of genomics and bioinformatics. Please contact Dr. Weihua Huang for the appointment. The service will be provided based upon the request order received.

Contacts:

Weihua Huang, Ph.D.
Lab Director
Department of Pathology, BSB Room 409
Ph: (914) 594-3928
Fax: (914) 594-4163
Email: weihua_huang@nymc.edu

Brahmaraju Mopidevi, Ph.D.
Assistant Lab Director
Dept. of Pathology, BSB Room 438B
Ph: (914) 594-4785
Fax:  (914) 594-4163
Email: bmopidev@nymc.edu

Humayun Islam, M.D., Ph.D. 
Interim Chairman of Pathology
BSB Room 413
Ph: (914) 594-4150
Fax: (914) 594-4163
Email: Humayun.Islam@wmchealth.org