Next Gen Sequencing
The facility provides high throughput sequencing on the Illumina NextSeq 500
, the Thermo Fisher Ion Torrent
PGM and Ion Proton sequencers. All three platforms offer rapid turnaround, with sequencing run times ranging from 2-29 hours. The NextSeq 500 can sequence 20 RNA-seq, or ChIP-seq libraries per day. The Ion Torrent is ideal for sequencing of small genomes and targeted sequencing of predefined gene sets. The NextSeq500 and the Ion Proton support several applications including, whole transcriptome, and whole exome sequencing.
Human cell line authentication and mycoplasma testing services
are available through the Genomics core. We use the GenePrint 10 System from Promega to preform short tandem repeat (STR) analysis on genomic DNA submitted to the core. STR data is processed by the core in GeneMarker HID, and allele calls are returned to the customer. For commercially available cell lines, the core will search STR profiles against databases of know STR profiles (ATCC, RIKEN, JCRB, and DSMZ) and return the best match.
Microarray based global analysis of human gene expression
is available on the Illumina BeadStation platform. Illumina has discontinued mouse and rat arrays, so for such gene expression analysis, contact Brian James
to discuss RNA-seq options. For human RNA samples, the facility confirms RNA quality, and then performs microarray analysis as well as initial data analysis. Array data are returned to the investigator, and if desired, also passed on to the Bioinformatics Core for more detailed analysis.
Quantitative real-time PCR (Q-PCR) service
is predominantly SYBR green-based analysis, but hybridization probe (e.g. TaqMan) approaches are supported. Starting with RNA, the facility will utilize primers from investigators, or design custom primers and perform Q-PCR. The facility provides control primers and assists with experimental design, as well as providing basic relative quantitation analysis. Q-PCR analysis in the facility can also provide gene, RNA, or viral copy number data.
Capillary DNA sequencing
is being outsourced, with three vendors picking up samples at SBP and typically returning results within 24 hr.