Genome Technology Center Fees & Sample Submission Guidelines
At NYU School of Medicine’s Genome Technology Center, our scientists use sophisticated sequencing tools to provide investigators with optimal data. Researchers can submit cell samples through the mail or in person at our Manhattan laboratory. We provide detailed guidelines on the sample volumes and concentrations needed for a range of sequencing services.
Genome Technology Center Fees
See our price list.
Prices are subject to change. Interested parties are encouraged to contact us at firstname.lastname@example.org.
To send samples by mail, use this address:
Genome Technology Center
550 First Avenue, MSB 308
New York, NY 10016
Attn: Adriana Heguy
Dropping Off Samples
Researchers can drop off samples for any of our services at the address above from 11:00AM to 12:00PM, Monday through Friday, after submitting an iLab request.
Please submit your samples in a 96-well plate labeled with your name, lab, and date, and fill out the corresponding sample submission form with sample ID and well location in iLab. If you have performed quality control on your samples, bring or email us a copy of the results, even if we will also perform quality control.
Nucleic Acid Extraction
We accept samples from any extraction method, although TRIzol™ extractions are not recommended as they can carry over phenol and salt that affect some downstream applications. If TRIzol™ is necessary, we recommend column cleanups.
The Translational Research Laboratory provides nucleic acid extraction services.
Picking Up Samples
We can’t store samples or libraries for more than three months. We discard any samples or libraries that are not picked up within that period.
Sample Volume and Concentration Guidelines
For library preparation, sequencing, and related services, we follow manufacturers’ requirements.
Quality-Control Volume Requirements
For quality control without library preparation or sequencing, provide the following sample volume plus 1 μL or more to allow for pipetting errors:
- TapeStation: 2 μL
- Bioanalyzer: 1 μL
- NanoDrop™: 1 μL
- Qubit®: 1 μL (2 to 3 μL for very low chromatin immunoprecipitation sequencing [ChIP-seq] samples)
- quantitative polymerase chain reaction (qPCR): 3 μL
Note that all RNA must be free of DNA.
For TruSeq library preparation, provide the following:
- unstranded polyA or stranded messenger RNA (mRNA): 100 to 500 ng of DNase-digested total RNA in up to 50 μL water, RNA integrity number (RIN) > 8
- ribo-depletion: 100 to 500 ng of DNase-digested total RNA in 10 μL water (some degradation is acceptable)
For low-input RNA-seq, provide the following:
- Clontech: 50 pg to 10 ng of DNase-digested total RNA in 10 μL water
- NuGEN: 500 pg to 100 ng of DNase-digested total RNA in 5 μL water
Whole Genome Sequencing
For whole genome sequencing, provide the following:
- KAPA DNA preparation: 1 μg (if less, PCR is required in library prep)
For ChIP-seq, provide the following:
- KAPA Hyper preparation: 1 to 50 ng in up to 50 μL water
- Rubicon ThruPLEX®: 50 pg to 50 ng in 10 μL water
For exome sequencing, provide a minimum of 250 ng of DNA.
For assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) using fresh cells, contact Adriana Heguy, PhD, director, at email@example.com, or Ram Ramaswami, PhD, assistant research scientist, at firstname.lastname@example.org, to plan your experiment in advance. We can make libraries from different cell numbers.
16S Library Preparation
For 16S library preparation, contact automation manager Peter Meyn at email@example.com with questions. We require a minimum 10 μL template per sample supplied in a 96-well format. You are responsible for supplying the forward and reverse primers. Label your sample with the desired PCR reaction and thermocycling conditions.
Quality control of all PCR products is performed using Agilent Technologies’ TapeStation. Unless otherwise specified, we use equimolar pooling of samples. A 10 percent PhiX spike-in is added to all libraries for necessary diversity; if your requirements differ, please specify.
For Nanostring analysis, please provide the following:
- mRNA: 100 ng total RNA in 5 μL water
- micro RNA (miRNA): 100 ng total in 3 μL water
Droplet Digital PCR
For Droplet Digital™ PCR, sample requirements depend on the scope and protocol. Email us at firstname.lastname@example.org to discuss your project.
C1 Auto Prep from Fluidigm
For C1™ Auto Prep from Fluidigm, contact Dr. Heguy at email@example.com or Yutong Zhang, MS, assistant research scientist, at firstname.lastname@example.org well in advance of your experiment to discuss the details of your project. As a general rule, cells should be at single-cell suspension and about 400 cells per μL in 20 μL water.
10x Genomics Chromium for Single-Cell Library Preparation
If you have questions about our MiSeq services, email Mr. Meyn at email@example.com.
For V2 chemistry, provide a 50-cycle kit, 300-cycle kit, or 500-cycle kit. Nano or micro kits are available upon request for 300-cycle kits and 500-cycle kits.
For V3 chemistry, provide a 150-cycle kit or 600-cycle kit.
MiSeq Sample Requirements
For prepared libraries, provide a minimum of 10 μL at 2 nM. If you require library quality control, provide additional volume per our quality-control volume requirements.
For MiSeq requests, provide the following information:
- chemistry: 50-cycle kit, for example
- sequencing parameters: single read or paired end plus length (SR50 or PE300, for example)
- required primers: specify standard Illumina primers or primers that you supply
- library diversity: low-diversity libraries require PhiX spike-in (5 to 25 percent)
- sample sheet: specify sample names and bar code information in digital format, such as .csv or .xlx.
For prepared libraries, we require a minimum of 10 μL at 2 nM. We highly recommend library quality control by our staff prior to sequencing, which includes TapeStation and Qubit® or qPCR, depending on the library type and whether we do pooling or you do it. Please see our quality-control volume requirements for guidelines.
For HiSeq requests, provide the following information:
- sequencing parameters: single read or paired end read + length (SR50 or PE100, for example) and number of lanes
- sample sheet: specify sample names and bar code information in digital format
If you submit completed libraries for sequencing that have been run using your quantification (meaning that we did not perform qPCR) and results are suboptimal (lanes were under- or overclustered), you accept the sequencing data as is. If we repeat any lanes, you are charged at full price.
If we run qPCR in-house on completed libraries and results fall below the Illumina-accepted pass rate, we will repeat the lane free of charge.
Please note that performing quantification on a library pool will affect only the cluster density of the sample on the HiSeq. It does not guarantee even reads for all samples in the pool.