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
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.
| Measure | MiSeq Reagent v2 | MiSeq Reagent v3 | ||
|---|---|---|---|---|
| Read Length | 1 x 50 bp | 2 x 250 bp | 2 x 75 bp | 2 x 300 bp |
| Total Time | ~5.5 hrs | ~39 hrs | ~21 hrs | ~56 hrs |
| Reads | 12-15 million | 22-25 million | ||
| Output | 0.75-0.85 Gb | 7.5-8.5 Gb | 3.3-3.8 Gb | 13.2-15 Gb |
| Measure | NextSeq Mid-Output | NextSeq High-Output | ||
| Read Length | 2 x 75 bp | 2 x 150 bp | 2 x 75 bp | 2 x 150 bp |
| Total Time | ~15 hrs | ~26 hrs | ~18 hrs | ~29 hrs |
| Reads | up to 130 million | up to 400 million | ||
| Output | 16.25-19.5 Gb | 32.5-39 Gb | 50-60 Gb | 100-120 Gb |
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 (2x75 bp) | $1,297 | $1,362 |
| Mid-Output 300 bp sequencing (2x150 bp) | $2,090 | $2,195 |
| High-Output 150 bp sequencing (2x75 bp) | $3,410 | $3,581 |
| High-Output 300 bp sequencing (2x150 bp) | $5,462 | $5,735 |
| MiSeq Service | Internal | External |
|---|---|---|
| V2, 50 bp sequencing (1x50 bp) | $980 | $1,029 |
| V2, 500 bp sequencing (2x250 bp) | $1,410 | $1,481 |
| V3, 150 bp sequencing (2x75 bp) | $1,088 | $1,142 |
| V3, 600 bp sequencing (2x300 bp) | $1,841 | $1,933 |
| Library Prep Service | Internal | External |
|---|---|---|
| TruSeq mRNA (polyT purification) | $160 | $192 |
| TruSeq mRNA (RiboZero purification) | $275 | $330 |
| TruSeq small RNA | $300 | $360 |
| Nextera XT | $100 | $120 |
| Others Service | Internal | External |
|---|---|---|
| Bioanalyzer 2100 (DNA or RNA, per sample) | $15 | $20 |
| TapStation 4200 (DNA or RNA, per sample) | $12 | $15 |
| BluePippin (size selection, per sample) | $25 | $30 |
| Stratagene Mx3005p Real-time PCR | inquire | inquire |
| Spectramax Gemini XPS | inquire | inquire |
| Fluorometer 96-well | inquire | inquire |
| Biomek FXp (automation system) | inquire | inquire |
Visit, Consults and Service Requests
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. Brahmaraju Mopidevi for an appointment. Services will be provided based upon the request order received.
Contact
Ravi Sachidanandam, Ph.D.
Director, Genomics Core Lab
Dept. of Pathology, Microbiology and Immunology
Basic Sciences Building Room 408
Phone: (516) 527-4452
Email: rsachidanandam@nymc.edu
Lab Leadership
Humayun Islam, M.D., Ph.D.
Chairman of Pathology, Microbiology and Immunology
Basic Sciences Building Room 413
Phone: (914) 594-4150
Fax: (914) 594-4163
Email: humayun.islam@wmchealth.org
