The ISCRM Genomics Core features the most advanced sequencing capabilities available today. Our sequencing instrumentation, including the latest equipment from 10X and Illumina, produces the highest quality, unbiased possible data about gene expression, regulation, and cell behavior. Whether you are interested in single-cell genomics or spatial genomics, our staff is here to provide the training and experimental design support you need to achieve your research objectives.
The ISCRM Genomics Core is available to all ISCRM faculty members and trainees. We are located in the Quellos Core space on the second floor of the N Building on the South Lake Union campus.
Pipeline – From Cells to Data Output
The ISCRM Genomics Core provides a full sequencing pipeline, from tissue or single cells to analysis. The pipeline includes a 10x Chromium with Visium capabilities for library generation and cell encapsulation and an Agilent TapeStation 4200 for quality control, sequenced by an Illumina NextSeq 2000 capable of reads in the 400 million to 1.1 billion range. The final data output is analyzed by a full featured range of applications hosted on a ISCRM reserved node of the UW Hyak supercomputer.
Using the Equipment – What to Expect
The ISCRM Genomics Core provides all the equipment needed to perform all of the pipeline steps. The end-user only needs to provide consumables such as plastics, reagents, and the kits and cartridges from 10x, Agilent, and Illumina.
The instrumentation is complex, but Genomics Core staff will guide you through the process. The TapeStation also provides checks during several parts of the pipeline, catching user mistakes before expensive parts are used. The Visium system pairs nicely with the ISCRM Histology center, and allows for high quality sectioning.
Once the library generation is complete and cells are barcoded for the sequencer, use of the Illumina NextSeq 2000 is relatively straightforward – simply do the math for the number of cells per sample, how many samples, and the desired saturation (gene coverage). Once that is determined you pool your samples, place the pool into the cartridge, and the run starts. It takes 20-40 hours to generate 300GB-1TB of data, which is then transfered to the ISCRM Hyak node where the end-user can analyze the data according to the specifications desired, resulting in an unbiased, high quality data output.
Slack channel (user-driven knowledge base)
Kits available from 10X (Quotes in DropBox):
3’ Chromium NextGEM Library & Gel Bead Kit
5’ Chromium NextGEM Library & Gel Bead Kit
ATAC Chromium NextGEM Library & Gel Bead Kit
Visium Spatial Gene Expression Slide & Reagent Kit
Kits available from Illumina (Quotes in DropBox):
(Definitions: P2 is 400 million reads. P3 is 1.1 billion reads. Cycles and base pairs read are 1:1 in quantity)
P2 100 Cycle Kit
P2 200 Cycle Kit
P2 300 Cycle Kit
P3 100 Cycle Kit
P3 200 Cycle Kit
P3 300 Cycle Kit
Annual Chromium/Visium kit giveaway (November Deadline)
Multiome ATAC + 3’ Grant (3/21/21 Deadline)