The Laboratory is equipped with the necessary experimental and bioinformatics infrastructure to generate, store, and analyze large-scale datasets from Illumina NextSeq2000 high throughput sequencer and from the Oxford Nanopore MinION platform. Shared equipment hosted at MMJGGL is accessible to the Caltech community.
The Illumina NextSeq2000 is a scalable platform that provides four output levels to accommodate studies of varying sizes. The P1 flowcell generates 100 million reads and delivers rapid results, enabling efficient processing of a limited number of samples. The P2 flowcell, capable of producing 400 million reads, is well-suited for medium-sized projects. The P3 and P4 flowcells have yields of 1.2 and 1.8 billion reads, respectively, and are used for larger studies with a greater number of samples or when the highest depth of coverage is required. With 14 kit configurations and read lengths ranging from 1 x 50 bp to 2 x 300 bp, NextSeq2000 offers broad platform utility with flexibility to expand application and scale efficiently.
Long read sequencing services are offered using the Oxford Nanopore MinION platform. MinION utilizes a flowcell-integrated ASIC sensor chip for data acquisition and control to achieve read lengths up to 4 Mb and data yields up to 50 Gb per flowcell, enabling a broad range of applications. The latest flowcell design and sequencing chemistry deliver simplex reads of Q20+ accuracy and duplex reads of close to Q30 accuracy. Neural network-based basecalling models can accurately detect base modification in both DNA and RNA from the native nanopore signal, eliminating the need for specialized library preparation procedures. Currently, the detection of 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), N4-methylcytosine (4mC) and N6-methyladenosine (6mA) is supported for DNA, while N6-methyladenosine (6mA) and pseudouridine (pseU) are detected in RNA.
In addition to providing sequencing services, MMJGGL hosts a range of instruments that are available to Caltech researchers. These include Agilent 2100 Bioanalyzer, Qubit fluorometer, Nanodrop ND-1000 spectrophotometer, Agilent G2565 Microarray Scanner, Applied Biosystems ViiA 7 and Roche LightCycler 480 II Real-Time PCR instruments. The shared equipment is reserved through the Clustermarket booking system and is free to use. To request a Clustermarket account, please contact Igor Antoshechkin.