Genome Technology Center Fees & Sample Submission Guidelines

Genome Technology Center Genome Technology Center Fees & Sample Submission Guidelines
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Genome Technology Center 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 genomics@nyumc.org.

Mailing Samples

To send samples by mail, use this address:

Genome Technology Center 550
First Avenue, MSB 308
New York, NY 10016
Attn: Adriana Heguy
212-263-8048

Dropping Off Samples

Researchers can drop off cell samples at the address above from 11:00AM to 12:00PM, Monday through Friday.

Please number your samples for easy reference. Include your initials or other code in the sample names. We do not accept samples numbered “1. . . 24” or “A. . .H.” 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.

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.

RNA-seq

For TruSeq library preparation, provide the following:

  • unstranded polyA or stranded messenger RNA (mRNA): 100 to 500 ng in up to 50 μL water, RNA integrity number (RIN) > 8
  • ribo-depletion: 100 to 500 ng in 10 μL water (some degradation is acceptable)

For low-input RNA-seq, provide the following:

  • Clontech: 50 pg to 10 ng in 10 μL water
  • NuGEN: 500 pg to 100 ng 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)

ChIP-seq

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

Exome Sequencing

For exome sequencing, provide a minimum of 250 ng of DNA.

ATAC-seq

For assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) using fresh cells, contact Adriana Heguy, PhD, director, at adriana.heguy@nyumc.org, or Ram Ramaswami, PhD, assistant research scientist, at sitharam.ramaswami@nyumc.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 peter.meyn@nyumc.org 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.

Nanostring Analysis

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 genomics@nyumc.org to discuss your project.

C1 Auto Prep from Fluidigm

For C1 Auto Prep from Fluidigm, contact Dr. Heguy at adriana.heguy@nyumc.org or Yutong Zhang, MS, assistant research scientist, at yutong.zhang@nyumc.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

Please contact Ms. Zhang at yutong.zhang@nyumc.org or Mr. Meyn at peter.meyn@nyumc.org to arrange a meeting to discuss your specific experiment. We can use 500 to 12,000 cells per experiment.

MiSeq

If you have questions about our MiSeq services, email Mr. Meyn at peter.meyn@nyumc.org.

MiSeq Chemistries

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.

MiSeq-Required Information

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.

HiSeq

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.

HiSeq-Required Information

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

HiSeq Results

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.