At NYU Langone’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

Our list of services and prices is available on iLab. You can register for an iLab account if you do not have one. This is a one-time registration process that enables users to access all NYU Langone core laboratories.

Mailing Samples

To send samples by mail, use this address:

Genome Technology Center
550 First Avenue, MSB 286
New York, NY 10016
Attn: Adriana Heguy
212-263-5743

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.

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:

• Enriched polyA or Total RNA: 100 to 1,000 ng of DNase-digested total RNA in up to 50 μL water, RNA integrity number (RIN) > 8
• ribo-depletion: 100 to 1,000 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
• Tecan Revelo: 500 pg to 25 ng of DNase-digested total RNA in 8 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)
• Illumina DNA Prep PCR-free: 200-500 ng in 30μL volume
• Illumina 1/4 scaled DNA Prep: 5-500 ng in 30μL volume (has PCR step)

ChIP-seq

For ChIP-seq, provide the following:

• KAPA Hyper preparation: 1 to 50 ng in up to 50 μL water
• Takara ThruPLEX^®: 50 pg to 50 ng in 10 μL water

Exome Sequencing

Illumina DNA prep with enrichment human exome v2.0 or v2.5

• gDNA 500-500 ng in 30 μL volume
• FFPE DNA 100-500 ng in 30 μL volume

Custom Capture Panel

Can perform custom capture panels from IDT to Twist Biosciences

ATAC-seq

For assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) using fresh cells, contact Paul Zappile, MS, research scientist, at Paul.Zappile@NYULangone.org, to plan your experiment in advance. We can make libraries from different cell numbers. Typical submission range in 50k up to 1 million cells per sample.

16S Library Preparation

For 16S library preparation, contact automation manager Peter Meyn at Peter.Meyn@NYULangone.org with questions. We require a minimum 10 μL template per sample supplied in a 96-well format. You may supply your own forward and reverse primers or for an additional charge utilize primers provided by the GTC. In your iLab request please specify the desired PCR reaction concentrations and thermocycler amplification 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@NYULangone.org to discuss your project.

Single-Cell Library Preparation

The GTC offers both the 10x Genomics chromium platform and Fluent BioSciences PIP-Seq technology.

Please contact Ms. Zhang at Yutong.Zhang@NYULangone.org or Mr. Meyn at Peter.Meyn@NYULangone.org to arrange a meeting to discuss your specific experiment. Typical loading is 500 to 15k cells per experiment but amounts up to 60k are possible with the inclusion of a hashing strategy.

General Details:

10x: 3', 5', ATAC and Multiome protocols are offered.

PIP-Seq: T2, T20, and T100 kits are available.

MiSeq

If you have questions about our MiSeq services, email Mr. Meyn at Peter.Meyn@NYULangone.org.

MiSeq Chemistries

For V2 chemistry, the GTC has 50-cycle kits, 300-cycle kits, or 500-cycle kits available. 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 custom primers (provided by researcher)
• 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.

NovaSeq X-plus

For prepared libraries, we require a minimum of 20 μL with at least 2 nM concentration per lane (higher concentration preferred). 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.

Novaseq X-plus-Required Information

For Novaseq X-plus requests, provide the following information:

• sequencing parameters in ilab: all runs are paired using 100, 200, 300 cycles
• single read runs can be done but you must use the entire flow cell
• sample sheet: specify same names and corresponding barcode sequence in excel format (example template available in iLab request)

Novaseq 6000-Required Information

• sequencing parameters in ilab: all runs are paired using 100, 200, 300 cycles
• single read runs can be done but you must use the entire flow cell
• if providing a pool to run, please provide at least 100 μL of greater than 2nM concentration for SP & S1 flow cells. S2 required volume is 150μL and S4 volume is 310μL. An additional Lane separation kit can be used for all flow cells to split lanes due to repeating index adapters- this is a small additional charge.

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 of the HiSeq. It does not guarantee even reads for all samples in the pool.