Planning your experiment

Please contact the GHTF to schedule a consultation about experimental design and the time frame of your experiment.

Depending on your needs, GHTF can prepare mRNA, scRNA, small RNA, genomic, ChIP, methyl and exome sequencing libraries. GHTF staff have experience with multiple strategy options for exome enrichment, ribosomal RNA depletion and generation of multiplex libraries in order to insure maximal return of data from experiments. The GHTF is equipped with a Covaris S220 focused sonicating shearer; Sage Sciences Blue Pippin electrophoresis system for DNA sizing and protein fractionation, NanoDrop 1000 and One Spectrophotometer, Qubit 1.0 and 3.0 fluorometers, MJ Research Tetrad thermal cycler, Agilent 2100 Bioanalyzer, and Agilent MX PRO RTPCR to facilitate the preparation of libraries and quality testing and final titration of samples. The Fluidigm C1 single cell autoprep and the 10X Genomics Chromium systems for capturing single cells and preparing templates are available for single cell genomic applications. For higher throughput single cell analysis, the 10x Genomics Chromium is available for single cell RNA 3’-end sequencing or genome and exome DNA sequencing. The Affymetrix microarray platform is utilized for gene expression studies, and analyzing known DNA SNPs and CNVs. Sequencing is currently performed using the Illumina sequencers, HiSeq 2500 with a dual mode system for either high output or rapid mode sequencing, HiSeq 4000 and MiSeq. For long reads, the GHTF offers Pac Bio Sequel long-read sequencing, a capability that is useful for whole genome assembly; targeted RNA sequencing for identification of alternative splice variants; targeted DNA sequencing for haplophase genotyping, and for direct sequence identification of base modifications. Digital gene expression and miRNA analysis is performed on the NanoString. Long-range genome optical mapping for genome assembly or identification of structural variants is performed on the BioNano Irys system.