Services
gCore is now accepting sample submissions for library preparations and sequencing using the PacBio Revio long-read sequencer.
Bulk Isoform RNAseq (IsoSeq)
Single-cell Isoform RNAseq
Genomic DNA
The Revio is used for detecting splice isoforms and their differential expression in RNA, as well as structural variants, haplotypes, phasing, methylation, CRISPR mutations, and viral insertions in DNA. These are tasks challenging to accomplish with short-read sequencing.
Revio's output is 60-90 Gbps per SMRT cell, equivalent to over 20x-30x human genome coverage. We have the capacity to run 4 SMRT cells per 30 hours. This allows sequencing of 12-18 kb fragments, multiplexing of samples, or splitting the samples into multiple SMRT cells.
Do you need your sequencing data analyzed and graphs prepared for publications and grants? The SCRM Genomics Core has partnered with experienced bioinformaticians and now offers comprehensive computational genomics services at competitive rates, including differential expression analysis, variant calling, pathway/network analysis, genomic data visualization, and sequence assembly.
Email Max or book a slot on our booking page to schedule a complimentary consultation. Read more
The advantage of short reads by Illumina is that the pricing of these recently decreased following the acquisition of the Illumina NovaSeqX+ by the UCSD IGM Genomics Center. The advantage of enzymatic over bisulfite sequencing is that bisulfite damages DNA and its timing needs to be calibrated at every experiment to avoid excessive conversion, while enzymatic is gentle on DNA and offers higher specificity with no requirement for calibration.
You submit 5-250ng of purified genomic DNA per sample. gCore prepares the libraries and sequences them at IGM. You get back the sequencing data in which unmethylated C is converted to T. By comparing the data to the reference genome, the positions of methylated cytosines are determined. Additionally, bioinformatic analysis is also offered by gCore.
NEB and Illumina support
Nanopore ONT long-read sequencing
DNA and RNA long read sequencing, methylation analysis, 5mC and 5hmC.
Data storage
$5/TB/month, free support, auto-upload/download, mounted drive access, full backup, multiple protocols, NextCloud/Ubuntu hosting.
10x Genomics Chromium X for single-cell whole genome analysis
Bulk and single-cell library prep pricing, RNAseq and ATACseq
Available as both self-service or full library preparation starting from dissociated tissue/cells.
To run samples on the Chromium X, you need to book a time on FBS. Once booked, you can start with organoids, tissue, or cell cultures and prepare single-cell suspensions. Prepare the sample with the appropriate 10x kit (all kits can be run on the Chromium X at SCRM), and use 10x Chromium X to partition cells and 10x barcoded gel beads into nanoliter Gel Beads-in-Emulsion (GEMs). Each cell is barcoded for whole genome or transcriptome analysis. These libraries can be sequenced on any applicable sequencer, such as the NextSeq 2000. The genomics core can help with planning the sequencing run and data analysis.
Bulk Library Preparation and DNA/RNA Extraction
Bulk and single-cell library prep pricing
The SCRM Genomics Core provides library preparation services to meet all of your sequencing needs. In addition to library preparation for long-read sequencing, we offer all forms of short-read library preparation. If you require a service not listed, Ask Trevor and we can accommodate your needs.
Any libraries prepared by the genomics core can either be sequenced in-house, or sent to another facility for sequencing. The genomics core will handle all logistics associated with this process, so you can get your results hassle-free.
DNA/RNA extraction
High Molecular Weight DNA extraction for long-read sequencing from the rodent spleen and other tissues: $135 per sample, for 4+ samples. Submit 2-5 mg of tissue for PacBio Revio. For some tissues, additional optimization may be required, please ask Trevor.
DNA extraction for short-read methylation analysis: approximately $35 per sample from cell lines, and $135 per sample from tissue, for 4+ samples, please inquire.
RNA extraction for Revio IsoSeq: approximately $35 per sample, and $135 per sample from tissue for 8+ samples, please inquire.
Ask Trevor any questions.
NextSeq 2000 Illumina Short-Read Sequencer
Bulk and single-cell library prep pricing
Sequencer self-service Pricing
The genomics core can also run your samples for no additional cost.
The genomics core also has a MiSeq for self-service. There is a $200 usage fee for recharge.
The NextSeq 2000 represents a high-throughput next-generation sequencing system, boasting a capacity of up to 300 Gb and a maximum of 1 billion reads per run. With 50, 100, 200, 300 and 600 cycle options, it permits robust de novo assembly and differential expression analysis. The system's compatibility with dual-index barcoding augments multiplexing capacity, making it suitable for single-cell RNA sequencing (scRNA-seq) experiments that require high-throughput analysis and precise resolution of cellular heterogeneity. The NextSeq 2000 allows for a rapid turnaround and data analysis using the onboard DRAGEN analysis pipeline.
Andor Dragonfly Spinning Disc Confocal Microscope
Training and self-service are offered. Dragonfly training videos and rules.
The Andor Dragonfly 200 spinning disc confocal microscope provides high-speed, high-resolution imaging. Its configuration includes 10x and 20x dry, 40x water, and 63x glycerol objectives, alongside an additional 2x camera magnification, supporting subcellular level imaging. As a spinning disc system, the Dragonfly 200 allows for rapid image acquisition, making it an essential tool for real-time single-cell and molecular analyses. This instrument is able to accommodate live imaging of slides or wells.
Imaris
Imaris workstation is a commercial alternative to ImageJ, allowing automation of 3D reconstruction of cells, neurons, axons, dendrites, and vessels and also allowing automatic quantification of cells, nuclei, synapses, contact points, volumes and intensities.
Micropatterned heart organoid progenitor. Green - pluripotency marker, red - actin, and blue - nuclei. We thank Tom Molley from Adam Engler's lab for the image taken on Andor Dragonfly 200 microscope.
Nanostring GeoMX
The GeoMx Digital Spatial Profiler (DSP) by NanoString enables high-plex spatial profiling of RNA and protein molecules within a tissue sample. It uses Digital Optical Barcoding Technology to quantify up to 800 targets per region while preserving tissue morphology. The GeoMx DSP allows researchers to select regions of interest and maintain spatial context during high-resolution, high-throughput analysis, providing an effective tool for understanding spatial heterogeneity within tissue samples at the molecular level.
Nanostring GeoMX spatial genomics profiler
DNA/RNA Quality Control
Agilent TapeStation 4200
The Agilent TapeStation 4200 system is an automated electrophoresis solution for the sample quality control of DNA and RNA samples. The system integrates an instrument, data processing software, reagents, and ScreenTape devices specific for DNA and RNA. It is suitable to analyze size, quantity, and integrity of your samples. It fits for example in a next-generation sequencing (NGS) or biobanking workflow with low to high throughput delivering highly precise analytical evaluation. The TapeStation 4200 is capable of running up to 96 samples in a single run, allowing for a higher throughput than ever before. High Sensitivity D1000, High Sensitivity D5000, High Sensitivity RNA, and Genomic DNA ScreenTapes and reagents are stocked by the core. Their use is included in the recharge cost of $8 per sample.
Agilent Femto Pulse
The Agilent Femto Pulse is a pulsed-field capillary electrophoresis device capable of accurately sizing DNA and RNA. Due to the pulsed-field capabilities of the instrument, the Femto Pulse can size high-molecular-weight DNA up to 165 kb in length. Additionally, the instrument only requires <10 pg/uL of sample, minimizing the amount of sample required for sizing quality control. This instrument is not available for self-service; contact gcore@health.ucsd.edu to plan a run. The UCSD cost is $150 per run, and one run can accommodate up to 11 samples.