Next Generation Sequencing

Overview

High-throughput sequencing is an extremely fast developing technology that has profoundly altered our understanding of biology, human diversity, and disease.

Suzanne Alarcón

Sequencing Core Director

Services

Please acknowledge the use of the Sequencing Core Facility at the La Jolla Institute in publications. In addition, the NovaSeq 6000 and the HiSeq 2500 were acquired through the Shared Instrumentation Grant (SIG) Program (S10) and must be cited for their use: NovaSeq 6000 S10OD025052 and HiSeq 2500 S10OD016262.

Instrumentation

Illumina Miseq

The baby brother to the popular Hiseq. It also uses Illumina sequencing by synthesis and can complete a 500 cycle paired-end run in a couple of days on its one-lane flowcell. Depending on the type of library, it can produce anywhere from 7M to 16M reads on a full Flowcell kit. If you are interested in a smaller amount of reads, Illumina also offers Nano and Micro version kits. The most popular applications for the Miseq are enriched/targeted samples, bisulfite treated, and amplicons.

Agilent 2200 Tapestation

The Tapestation is an automated electrophoretic-based nucleic acid / protein analyzer that is indispensible for QC steps in library prep for NGS. In comparison to Bioanalyzer, the Tapestation provides savings on consumables, faster and more accurate data, and is capable of high throughput processing of 96-well plates. The automated loading reduces user error and the potential to waste precious samples. The pre-cast gel strips provide scalable throughput at a constant cost per sample, therefore it makes an excellent solution for high throughput and also eliminates unnecessary costs associated with low sample numbers.

Covaris Model E220

Currently, Covaris technology is the gold standard for fragmenting DNA in order to get a consistently tight size range. Although we use the Covaris E220 primarily for Chromatin shearing and fragmenting DNA in our library preparation pipeline, it has many other uses. The instrument achieves a high level of consistency and efficiency through its use of isothermal processing and the proprietary Covaris Adaptive Focused Acoustic technology. It can process 1 to 96 samples in a single batch, which is much more efficient than using our S2 model for large arrays of samples.

Beckman Coulter Biomek FXP

The La Jolla Institute is currently engaged in a partnership with Beckman Coulter and Illumina for the purposes of developing and validating Illumina library preparation methods on the Biomek FXP automation platform. Currently, we have the Truseq mRNA Stranded, Truseq Nano DNA and Nextera based protocols installed on the system. Implementing automation for library preparation should reduce inconsistency and risks associated with human errors. The ability to generate libraries, either from a single sample to as many as 96 at a time, will benefit both small-scale and particularly large-scale experiments. We wish to keep a long-standing intimate relationship with both Illumina and Beckman Coulter to continue improving our and other’s NGS needs.

NovaSeq 6000

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Rates

Technical Training and Assistance

	INSTITUTE AFFILIATE	3RD PARTY NON-PROFIT	3RD PARTY FOR-PROFIT
Technical Training – Sequencing and Library Prep Specialist (per hour)	$66.15	$72.77	$121.05
Technical Assistance (per hour)	$44.10	$48.51	$80.70

Sample Prep and QC

	INSTITUTE AFFILIATE	3RD PARTY NON-PROFIT	3RD PARTY FOR-PROFIT
Qiagen Full Service RNA Extraction (Trizol, per 12 samples)	$352.80	$388.08	$645.62
Qiagen Instrument Fee per 12 samples (does not include reagents)	$55.13	$60.64	$100.88
Tapestation Self-Service Full Tape (after Core training, reagents not supplied)	$33.60	$36.96	$61.49
Tapestation HS Screen Tape (15 samples + ladder, full service)	$162.75	$179.03	$297.83
Tapestation (non-HS) Screen Tape (15 samples + ladder, full service)	$131.25	$144.38	$240.19
Tapestation RNA Screen Tape (15 samples + ladder, full service)	$140.70	$154.77	$257.48
Qubit Quantification 8 samples – Self Service (does not include reagents)	$11.03	$12.13	$20.18
Qubit Quantification 8 samples – Full Service (includes reagents)	$35.83	$39.41	$65.57
Picogreen Quantification 96 Plate – Full Service	$89.03	$97.93	$162.92
Bead cleanup, Tapestation and Qubit QC, single sided	$62.40	$68.64	$114.19
Bead cleanup, Tapestation and Qubit QC, double sided	$85.72	$94.29	$156.87
Library Pool QC (Qubit, Tapestation, qPCR – Required for every partial FC submission, per library/pool)	$38.85	$42.74	$71.10
Library pooling, per sample up to 16 samples (includes fluorescence-based quant)	$15.75	$17.33	$28.82
Library pooling high/low samples, per sample (includes normalization and fluroescence-based quant)	$26.25	$28.88	$48.04

Library Prep

	INSTITUTE AFFILIATE	3RD PARTY NON-PROFIT	3RD PARTY FOR-PROFIT
Illumina Stranded mRNA-seq Library Prep (Each sample, first 16 samples)	$178.50	$196.35	$326.66
Illumina Stranded mRNA-seq Library Prep (Each samples, 17-96 in plate)	$152.88	$168.17	$279.78
Ultra low input RNA-seq (using SMARTer Stranded methods) (Each sample, first 16 samples)	$286.65	$315.32	$524.57
Ultra low input RNA-seq (using SMARTer Stranded methods) (Each sample, samples 17-96)	$200.66	$220.72	$367.20
DNA-seq Library Prep (Each sample, first 16 samples)	$138.36	$152.20	$253.21
DNA-seq Library Prep (Samples 17-96)	$87.58	$96.34	$160.28
PCR-free DNA-seq Library Prep Add-on, per sample	$82.69	$90.96	$151.32
10X Genomics Single Cell RNA GEX 3′ Library Prep (each sample)	$2,039.63	$2,243.59	$3,732.51
10X Assay day (2 days per 3′ workflow)	$562.28	$618.50	$1,028.96
Additional 10X Chip	$330.75	$363.83	$605.27
10X Cell processing	$220.50	$242.55	$403.52

MiSeq Sequencing

	INSTITUTE AFFILIATE	3RD PARTY NON-PROFIT	3RD PARTY FOR-PROFIT
MiSeq Self Service (nano; after Core training, does not include reagents)	$168.00	$184.80	$307.44
MiSeq Self Service (v2, v3; after Core training, does not include reagents)	$336.00	$369.60	$614.88
MiSeq v2 Nano Kit 300 Cycle Full Flowcell	$882.99	$971.29	$1,615.88
MiSeq v2 Nano Kit 500 Cycle Full Flowcell	$958.18	$1,054.00	$1,753.47
Miseq v2 50 Cycle Full Flowcell	$1,576.69	$1,734.35	$2,885.33
Miseq v2 300 Cycle Full Flowcell	$1,882.30	$2,070.53	$3,444.61
Miseq v2 500 Cycle Full Flowcell	$2,050.87	$2,255.96	$3,753.07
MiSeq v3 150 Cycle Full Flowcell	$1,695.53	$1,865.09	$3,102.83
MiSeq v3 600 Cycle Full Flowcell	$2,526.27	$2,778.90	$4,623.07

NovaSeq Sequencing

	INSTITUTE AFFILIATE	3RD PARTY NON-PROFIT	3RD PARTY FOR-PROFIT
SP 100 Cycle Full Flowcell	$3,258.33	$3,584.17	$5,962.75
SP 200 Cycle Full Flowcell	$4,130.91	$4,544.00	$7,559.57
SP 300 Cycle Full Flowcell	$4,432.49	$4,875.74	$8,111.45
SP 500 Cycle Full Flowcell	$5,928.80	$6,521.68	$10,849.70
S1 100 Cycle Full Flowcell	$6,150.18	$6,765.20	$11,254.83
S1 200 Cycle Full Flowcell	$7,400.69	$8,140.76	$13,543.26
S1 300 Cycle Full Flowcell	$7,978.23	$8,776.05	$14,600.16
S2 100 Cycle Full Flowcell	$10,493.57	$11,542.93	$19,203.23
S2 200 Cycle Full Flowcell	$12,832.34	$14,115.57	$23,483.18
S2 300 Cycle Full Flowcell	$13,784.58	$15,163.04	$25,225.79
S4 35 Cycle Full Flowcell	$16,275.00	$17,902.50	$29,783.25
S4 200 Cycle Full Flowcell	$21,054.39	$23,159.82	$38,529.53
S4 300 Cycle Full Flowcell	$23,431.51	$25,774.66	$42,879.66
XP Workflow; 2 Lane	$395.69	$435.36	$724.11
XP Workflow; 4 Lane	$1,266.66	$1,393.33	$2,317.99

Bioinformatics

For more information, please visit the Bioinformatics page.

	INSTITUTE AFFILIATE	3RD PARTY NON-PROFIT	3RD PARTY FOR-PROFIT
Programming or Technical Support (per hour)	$143.06	$249.34	$272.50
Mapping (per hour)	$288.02	$313.95	$518.70
Differential Expression Analysis	$288.75	$503.25	$550.00
NGS FASTQ and QC	$110.25	$192.15	$210.00

Functional Genomics

	INSTITUTE AFFILIATE	3RD PARTY NON-PROFIT	3RD PARTY FOR-PROFIT
shRNA Cherrypick (16 or less)	$110.25	$121.28	$201.76
shRNA Cherrypick (17-96)	$330.75	$363.83	$605.27
siRNA Cherrypick (up to 96 wells)	$330.75	$363.83	$605.27
siRNA Cherrypick (up to 384 well)	$937.13	$1,030.84	$1,714.94

Contact

For all scheduling requests, please contact the Sequencing Team at ngs@lji.org.