Single Cell RNA-sequencing

10x Genomics Chromium technology partitions cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs) which contain uniquely barcoded beads.

Details
Our Single Cell RNA-sequencing service includes partitioning single cells on the Chromium Controller, generating libraries from the cDNA, and sequencing on the NovaSeq.  We can run Single Cell Gene Expression, Single Cell Immune Profiling, and Single Cell ATAC.  Complimentary sequencing data in fastq format and output files from the 10x software will be provided.  Please contact us for a detailed quote and to discuss your experiment.

Vendor: 10x Genomics

Whole Exome Sequencing

LIBRARY PREPARATION: Construction of libraries for Next-Generation Sequencing

We can build a customized project for you based on our consultant rate and pass-through supplies. Please contact us at the email below.

Details
The genomic DNA is sheared by the Covaris LE220 to a target insert size of ~350bp and assembled into a library constructed with unique dual indexes which are compatible with the NovaSeq.

Vendor: Roche

EXOME CAPTURE
To capture the protein coding region of the human genome

Details
Libraries are pooled into a capture reaction that contains biotinylated oligonucleotide probes to target specific regions of interest.  The biotinylated probe/target hybrids are pulled down by streptavidin-coated magnetic beads to obtain libraries highly enriched for the target regions.

Vendor: Roche

DATA PROCESSING & ANALYSIS
Complimentary sequencing data will be provided in the fastq format. Under certain circumstances, sequence alignment to a reference genome and variant calling can be provided for an additional charge. Consultation for the clinical genomic variant is also available for an additional charge. All additional services are subjected to availability.   Please contact us for further information.

Illumina Sequencing

NovaSeq 6000: Next-generation sequencing (NGS) for RNA-seq, whole genome, whole exome, and targeted DNA sequencing

Details
We offer sequencing runs on the SP, S1, S2, and S4 flow cells.  Please contact us for a detailed quote.

HiSeq 2500: We offer sequencing runs on the High-Output or Rapid flow cells.

Vendor: Illumina

Applied Biosystems Axiom Genotyping

Genotyping of single nucleotide polymorphisms (SNPs) and insertions/deletions (indels), targeted structural genomic variants, such as small intragenic deletions and duplications, and the detection of microbial organisms.

Details
We perform large-scale genotyping assays using the Beckman Coulter Biomek FxP Target Prep Express and the Applied Biosystems GeneTitan Multi-Channel Instrument.  We can run most 96-well Axiom array plates.

Vendor: Thermo Fisher Scientific

DNA Extraction

Our DNA extraction service prepares high-quality DNA samples from blood (up to 10 ml) and saliva.  The DNA samples will be returned to you for storage, processing, or shipment to collaborators.

Consultation

Please email us at IHGSeqCore@ucsf.edu to set up a one-on-one free consultation to discuss your project.

High Performance Computing & Data Storage

Learn about our HPC & Data Storage services