Genomics Core

The Scripps Research Genomics Core supports next-generation sequencing platforms from Illumina, Oxford Nanopore and Element Biosciences, and PacBio (via local collaborators). We are able to provide a wide range of sequencing solutions to optimize sequencing scale, budget and turnaround time.

In most cases, the sequencing will complete within seven to ten business days after the submission of prepared libraries which pass the initial quality check. If there are urgent sequencing needs, please directly reach out to the Genomics Core for assistance.

Data Release

Internal users:

• Demultiplexing and dispatch of sequencing data usually takes 1-2 business days after the sequencing run has completed and passed quality check.

• Submitters should receive an email from Genomics Core [email protected] providing SFTP links to sequencing data, together with the sample key information (when applicable).

• Please read the dispatch email carefully regarding the downloading instructions.

• Please note that complications during demultiplexing process (e.g., wrong barcode information provided, barcode clashes) will delay the sequencing data being released.

External users:

• Demultiplexing and dispatch of sequencing data usually takes 1-2 business days after the sequencing run is done and passed quality check

• For first-time external submitters, the Genomics Core will work with CCBB to create an AWS account (one-time $125 fee will be applied)

• Upon the data transfer verification with submitters using a small dataset, sequencing data will be dispatched and able to download. An email from Genomics La Jolla [email protected] will be sent to submitters with the detailed instructions.

• Please note that complications during demultiplexing process (e.g., wrong barcode information provided, barcode clashes) will delay the sequencing data being released.

Library Preparation is the first step toward next-generation sequencing and downstream bioinformatics analysis. Hundreds of NGS library preparation methods are available, each designed to suit specific experimental approaches, with a wide range of commercial kits and variations for each method. The Scripps Research Genomics Core provides robust and commonly used library preparation methods as “standard” services, featuring fixed pricing and clear expectations for turnaround time and performance. However, we encourage researchers to reach out with requests for protocols not listed, as we can often accommodate these through our Custom Services.

Depending on the sample volume, the library preparation and sequencing will complete within 10 to 15 business days after the submission of samples which pass the initial quality check. If there are urgent sequencing needs, please directly reach out to Genomics Core staff for assistance.

DNA sequencing

DNA-Seq methods vary based on the DNA fragmentation approach, the size of the target genome, the inclusion of PCR amplification during library preparation, and the use of mate-pair technology. We can accommodate both Illumina reagents and NEB for DNA library Preparation.

RNA Sequencing

RNA sequencing (RNA-Seq) is widely regarded as the gold standard for genome-wide gene expression analysis across various biological conditions. It also enables the detection of splice variants, transcriptome profiling, and the discovery of non-coding RNAs. To support diverse sample types, we offer a variety of RNA-Seq library preparation kits, including options for low-input and partially degraded samples, as well as kits for polyA enrichment or ribosomal RNA reduction. The Genomics Core provides a comprehensive RNA-Seq workflow, from RNA extraction and quality control (QC) analysis to sequencing. Downstream data analysis through streamlined pipelines can be facilitated by the bioinformatics core (CCBB).

High-throughput low-cost RNA-seq (JCseq)

The Genomics Core provides a high-throughput, cost-effective RNA-seq library preparation protocol for batches of 48 or more. For inquiries about the assay or project submissions, please contact Sean Wang ([email protected]) or Steve Head ([email protected]).

Data Release

Internal users:

• Demultiplexing and dispatch of sequencing data usually takes 1-2 business days after the sequencing run has completed and passed quality check.

• Submitters should receive an email from Genomics Core [email protected] providing SFTP links to sequencing data, together with the sample key information (when applicable). Please read the dispatch email carefully regarding the downloading instructions.

• Please note that complications during demultiplexing process (e.g., wrong barcode information provided, barcode clashes) will delay the sequencing data being released.

External users:

• Demultiplexing and dispatch of sequencing data usually takes 1-2 business days after the sequencing run is done and passed quality check

• For first-time external submitters, the Genomics Core will work with CCBB to create an AWS account (one-time $125 fee will be applied)

• Upon the data transfer verification with submitters using a small dataset, sequencing data will be dispatched and able to download. An email from Genomics Core [email protected] will be sent to submitters with the detailed instructions.

• Please note that complications during demultiplexing process (e.g., wrong barcode information provided, barcode clashes) will delay the sequencing data being released.

Single-cell genomics is a rapidly evolving technology that studies the genetic material of individual cells, allowing researchers to understand cellular diversity and function within a complex tissue. It provides insights into cellular heterogeneity, revealing unique gene expression patterns and mutations at the single-cell level. Currently the Genomics Core supports 10x Genomics applications using the Chromium X instrument as the matured mainstream platform. We are actively assessing new Single Cell Genomics technologies as they evolve to provide broader and more accessible applications for researchers.

Key 10X Feature

• Extensive experience in the comprehensive end-to-end process: cell suspension quality check, GEM generation, library preparation, thorough quality control, sequencing.

• Cutting-edge 10X instrument capable of analyzing hundreds to tens of thousands of cells in a single run. Ability to multiplex samples using 10x protocols such as CellPlex, Flex and the new GEM-X Universal 3’ and 5’ (On-chip Multiplexing) kits. Also available is the option to multiplex samples using BioLegend TotalSeq oligo-conjugated antibodies (hashtags).

• 10X libraries sequenced using either Aviti or Illumina Nextseq 2000, ensuring cost-effective sequencing and scalability for large projects.

• Assistance with experimental design and assay selection, including Feature Barcoding and CiteSeq.

• Additional support services are available on-campus through the Flow Cytometry Core.

Workflow

Data Release

Internal users:

• Demultiplexing and dispatch of sequencing data usually takes 1-2 business days after the sequencing run has completed and passed quality check.

• Submitters should receive an email from Genomics Core [email protected] providing SFTP links to sequencing data, together with the sample key information (when applicable). Please read the dispatch email carefully regarding the downloading instructions.

• Please note that complications during demultiplexing process (e.g., wrong barcode information provided, barcode clashes) will delay the sequencing data being released.

External users:

• Demultiplexing and dispatch of sequencing data usually takes 1-2 business days after the sequencing run is done and passed quality check

• For first-time external submitters, the Genomics Core will work with CCBB to create an AWS account (one-time $125 fee will be applied)

• Upon the data transfer verification with submitters using a small dataset, sequencing data will be dispatched and able to download. An email from Genomics Core [email protected] will be sent to submitters with the detailed instructions.
  Please note that complications during demultiplexing process (e.g., wrong barcode information provided, barcode clashes) will delay the sequencing data being released.

GeoMx Digital Spatial Profiler

NanoString’s GeoMx™ Digital Spatial Profiler (DSP) (now acquired by Bruker) merges traditional immunofluorescence methods with digital optical barcoding technology to conduct highly multiplexed, spatially resolved profiling experiments. In one process, DSP technology performs whole-slide imaging using up to four fluorescent stains to capture tissue structure and choose regions of interest for high-plex profiling. The DSP chemistry allows spatially resolved high-plex profiling of RNA and protein targets on tissue sample sections.

Some Key features of DSP include:

• Minimum sample requirement: RNA analysis from either formalin-fixed paraffin-embedded (FFPE) or fresh-frozen sections.

• Morphological context: whole-slide imaging with four colors to guide profiling.

• Digital quantification: dynamic range of up to 6 logs (base 10).

• Non-destructive processing helps preserve valuable samples.

Microarray Scanning

The Genomics Core can provide high resolution (0.5um) imaging of standard microscope slides using an Innopsys 1100AL scanner. This is applicable to most commercial microarray slide options, including DNA/RNA, protein, peptide and glycan microarrays. The scanner can accommodate standard microscope slides and scan/filter at 3 standard channels (488/FITC – 532/Cy3 – 635/Cy5-APC) .

Custom Microarray Fabrication

Using robotic handlers, we can distribute samples onto standard microscope slides in microvolumes from 1nL to 500nL. Contact microarray printing uses solid steel capillary microarray printing pins using a MicroGrid II array printer equipped with ArrayIT Stealth Microarray pins. Non-contact deposition is available using a Dispendix (I.DOT). Additionally, the Genomics Core fabricates the NCFG mammalian and bacterial glycan microarrays, producing the most comprehensive set of available to the public. 

Element Aviti

Illumina Nextseq200

Oxford Nanopore Minion

10X Genomics Chromium X (single cell)

NanoString (Bruker) GeoMX digital spatial profiler

Agilent Tapestation

Thermo Fisher Qubit

Thermo Fisher Fluoroskan Microplate Fluorometer

SpectraMax Mini Multi-Mode Microplate Reader

MicroGrid II contact microarray printer

Innoscan 1100AL confocal microarray scanner

Opentrons (OT-2)

Eppendorf epMotion 5075

SPT Labtech Mosquito HV

Bio-Rad QX200 digital droplet PCR

First-time internal users need to request access to the Genomics Core and submit a service request through ELAN INFINITY (Located in MyApps). Please follow the instructions listed within the ELAN INFINITY Scripps Genomics Core Submission Portal. There will be a link within the portal for you to download the Genomics Core Project Submission Sheet. 

Use the Genomics Core Project Submission Sheet to provide the technical information for your project. Email the completed form to [email protected] and your point of contact (POC) staff scientist. 

Sample drop-off

• Option 1: Bring your samples to the Genomics Core and hand off to the core staff
• Option 2: Leave your samples in the sample drop-off freezer located outside of MB-28. To use the sample drop-off freezer option, your samples must be in a box/bag, clearly labeled with your name, PI name, and drop-off date. Please take a picture of your samples in the freezer and email to John or Jessica.

First-time external users need to contact Sheila at [email protected] or 858-784-2084 to set up an IDEA ELAN INFINITY account.

Please follow the instructions listed within the ELAN INFINITY Scripps Genomics Core Submission Portal. There will be a link within the portal for you to download the Genomics Core Project Submission Sheet.

Use the Genomics Core Project Submission Sheet to provide the technical information for your project. Email completed form to [email protected] and your point of contact (POC) staff scientist.

Please note that our shipping address is different than our laboratory physical address. Shipments using the incorrect address may delay the project timeline. 

Shipping Address: 

Attn: (list your contact person at the Genomics Core Facility)
Genomics Core Facility
9060 Activity Rd Unit F
MB28
San Diego, CA 92126

• For research projects that utilize routine genomics core workflows, consultation and data processing (without data interpretation), we kindly request recognition in your publication or presentation.

• Depending on the journal’s requirements and the author’s preference, the Genomics Core may be acknowledged in the Acknowledgements section and/or the Materials and Methods section. However, we ask that the Genomics Core be acknowledged in at least one of these sections.

• If you need specific details on lab protocols and methods, sequencing parameters or analysis pipelines used for your project to write the Materials and Methods section, please contact the staff member at the Genomics Core.

• This work was supported by the resources and staff at the Scripps Research Genomics Core Facility.

• The authors acknowledge the Scripps Research Genomics Core Facility for providing resources that contributed to the research results reported in this paper.

• Sequencing was performed at the Scripps Research Genomics Core Facility.

• We thank the Scripps Research Genomics Core Facility for providing [insert service(s)] and technical support.

• [insert service(s)] was performed at the Scripps Research Genomics Core Facility.

• The Scripps Research Genomics Core Facility performed [insert service(s)] using [insert technology] according to the manufacturer’s specified protocol.

If the Genomics Core staff provided support beyond standard workflows, consultation or data processing—such as advanced training, custom sample preparation or in-depth guidance in experimental design—please acknowledge the core scientist(s) by name in addition to recognizing the Genomics Core itself.

Examples:

• The authors acknowledge the technical expertise and assistance of [insert name(s)] and the Scripps Research Genomics Core Facility for their contributions to this publication.

• The technical support of [insert name(s)] and the resources provided by the Scripps Research Genomics Core Facility are greatly appreciated.

• We thank [insert name(s)] from the Scripps Research Genomics Core Facility for their assistance with [insert service(s) or contribution].

• We acknowledge the Scripps Research Genomics Core Facility and [insert name(s)] for their contributions to [insert service(s) or contribution].

If the Genomics Core scientists contributed to your project by interpreting data, playing a significant role in project design, making notable intellectual contributions, writing parts of your manuscript, developing bioinformatics tools and pipelines, or performing innovative laboratory work, please include them as co-authors on any resulting publications, posters, reports or presentations. Additionally, the Genomics Core should be acknowledged in the Acknowledgements section. The final decision on co-authorship is determined by the PI on the publication.