Institute for Systems Genetics Facilities & Resources

Institute for Systems Genetics Institute for Systems Genetics Facilities & Resources
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Institute for Systems Genetics Institute for Systems Genetics Facilities & Resources

The infrastructure of NYU School of Medicine’s Institute for Systems Genetics fosters collaboration. The institute is equipped with instrumentation, robotic automation, and software for running high-throughput assays and screens.

Computing Cluster

The Institute for Systems Genetics operates a high-performance computing cluster for the shared use of institute members. Located in space managed by NYU Langone, our facility is a commercial-grade data center. Information is backed up daily to an offsite disaster recovery provider.

Each compute node has an Intel® Xeon® processor. The specs are as follows: 2×12C, 2.5 GHz, 128 GB error-correcting code RAM, 2×2 TB startup discs in a redundant array of independent disks (RAID) mirroring configuration. It also has a 3×2 TB drive in a RAID 0 striping configuration for local scratch space (temporary storage).

A local network server supplies 40 TB of storage space in a doubly redundant RAID 6 configuration and more than 1 PB of online space on an EMC Isilon® storage array. The cluster runs the Simple Linux Utility for Resource Management, or SLURM, and other bioinformatics tools and UNIX utilities for efficient work scheduling.

Automation Suite

The automation suite provides researchers with instrumentation for high-throughput DNA assembly, purification, and analysis. We foster collaboration among researchers and work closely with investigators, technicians, and students in both experimental design and data analysis. We handle experiments of any scale and can process 96-, 384- and 1,536-well plates. The higher-density plates allow our collaborators to maximize data collection and minimize reagent usage.

Instrumentation

SGI-DNA’s BioXp™ 3200 System is a DNA printer that allows for hands-free gene assembly in the lab.

Molecular Devices’ QPix™ 420 achieves high-throughput colony picking. It is capable of bacteria and yeast colony selection with both white light (3,000 colonies per hour) and fluorescence (2,000 colonies per hour).

EdgeBio’s Caliper SciClone liquid handler is highly flexible for a range of automated pipetting needs. It can accommodate plasmid DNA purification in a 96-well format, cherry picking, and plate replication or rearraying.

The qPCR Workcell by Hudson Robotics, the high-throughput centerpiece of the automation suite, is equipped with a Labcyte Echo® 550 acoustic liquid handler. It allows for the precise transfer of nanoliter volumes without pipette tip consumption. It also lets researchers analyze DNA and RNA.

The Cobra from Art Robbins Instruments is a bulk reagent handler for dispensing volumes as low as 300 nL. The Roche LightCycler® 1536 provides a fluorescence-based platform for real-time polymerase chain reaction amplification detection. Plates are passed among the instruments by two Hudson Robotics PlateCrane SciClops™ robotic arms.

Media and Glassware

A media and glassware facility is located at the Alexandria Center for Life Science’s Manhattan campus and is staffed by a full-time technician.

Scientific Cores and Shared Resources

Our faculty and staff have access to NYU School of Medicine’s scientific cores and shared resources. Managed by the Division of Advanced Research Technologies, these shared resources include flow cytometry and cell sorting; genome technology, including high-throughput sequencing with several Illumina sequencers; histopathology; immunohistochemistry; microscopy; proteomics; and short hairpin RNA screening. We also have a transgenic mouse and embryonic stem cell chimera facility.