Functional Genomics

Functional Genomics

Overview

New, sophisticated, and in some cases expensive technologies are required to be at the cutting edge of biomedical research. La Jolla Institute has invested heavily in new technologies to catalyze breakthroughs by our exceptionally talented research staff. One example is the Functional Genomics Center at LJI, which resulted from a highly competitive federal granting process aimed at re-invigorating the local research community.

Launched in 2011 with funding from the National Institutes of Health and the National Institute of Allergy and Infectious Disease, the Functional Genomics Center was founded to combine large-scale automation and high-throughput capabilities with gene disruption techniques to pinpoint the function of individual genes and find new ways to disrupt genetic triggers of disease.

RNA interference and CRISPR/Cas9
RNA—the chemical cousin of the DNA in our genes—was long thought of as merely a messenger, but scientists now recognize that RNA plays a powerful role in controlling gene activity. Originally discovered in the petunia plant, RNA interference quickly became a powerful laboratory tool for shutting down individual genes to discover their function. Similarly, CRISPR/Cas9 is another powerful RNA-based technology that allows scientists to manipulate gene expression by directly altering DNA. Researchers are also exploring how to use RNAi and CRISPR as therapeutic tools to inactivate specific genes that are at the heart of many diseases.

The Functional Genomics Center at the La Jolla Institute is one of only a handful of comprehensive functional genomics labs around the nation funded by the National Institutes of Health, and houses one of the world’s largest collections of RNAi and CRISPR/Cas9 reagents. These valuable resources, combined with state-of-the-art instruments and the expertise of LJI staff, allows biomedical researchers to survey the human genome with unprecedented speed and precision.

The sequencing of the human genome in the 1990s marked a revolution in the field of human biology. Today we’re in the midst of another revolution. Human genomics is transforming the way researchers study how individual genes function within a finely tuned network of waxing and waning gene activity. Armed with that knowledge we will be able to individualize prevention, diagnosis and treatment and thus improve human health.

The Center at LJI is not only focused on finding new treatments for immune-related diseases, but it provides a prestigious addition to San Diego’s research community that is open to researchers on the Torrey Pines mesa and elsewhere.

Resources

Open Biosystems GIPZ Mouse shRNA (Lentiviral) [CSHL shRNAmir 7.18]

Open Biosystems TRC Human shRNA (Lentiviral)

hORFeome V8.1 Library [CCSB-Broad Lentiviral Expression Library]

MISSION TRC Human shRNA Library (Lentiviral)

MISSION TRC Mouse shRNA Library (Lentiviral)

TransOMIC pMLP Human shRNA (Retroviral)

TransOMIC pLMN Human shRNA (Retroviral)

TransOMIC pMLP Mouse shRNA (Retroviral)

TransOMIC pLMN Mouse shRNA (Retroviral)

Services

  • Cherry Picked Clones (per plate)
  • Cherry Picked Clones (per clone set, < 17)
  • Plasmid Purification (per plate)
  • Sequence Verification (per plate)
  • DNA Quantitation and Normalization (per plate)
  • RNA Quantitation and Normalization (per plate)
  • Transfection, Selection, RNA Extraction (per plate)
  • Lentivirus and Retrovirus Production and Titer
  • Cell Transduction and Selection

Complex Projects

  • Full Genome Screening Service
  • Functional Subset Screening Service
  • Custom Projects

Instrumentation

Perkin Elmer Envision Microplate Reader

The Perkin Elmer Envision Microplate Reader is a high throughput microplate reader capable of reading a single well to 3456 well plate formats. Available detection technologies available include:

  • Prompt Fluorescence
  • Time-Resolved Fluorescence
  • Fluorescence Polarization
  • FRET
  • Enhanced Luminescence
  • Absorbance
  • AlphaScreen
  • AlphaLisa

LiCor Oydyssey SA

The Odyssey® Sa Infrared Imaging System offers two-channel infrared detection. The Odyssey SA can be used for both quantitative Western blots and plate-based assays such as the In-Cell Western™ Assay.

BD Fortessa

The BD LSRFortessa™ cell analyzer offers the ultimate in choice for flow cytometry, providing power, performance, and consistency. It has 4 lasers which allow up to 18 color detection.

Molecular Devices ImageXpress Micro

High content imaging system for visualization of subcellular events in microtiter plates.
Objective: 4X, 10X, 20X, and 40X
Fluorophores: Cy3, Cy5, Cy7, DAPI, GFP, FITC, Texas Red, CFP, YFP, and TRITC.

Available libraries:

  • Dharmacon siGenome siRNA collection (mouse and human)
  • Mission/TRC shRNA collection (mouse and human)
  • TransOmic shMir collection (mouse and human)
  • Lenti-ORFeome collection (human)
  • Biosettia miRNA mimic collection (human)
  • LENTICRISPR Gecko library (mouse and human)

Rates

  2018 Internal Rates 2018 External Rates
CRISPR
LentiCRISPR Production $225.00 $425.25
RetroCRISPR Production $315.00 $595.35
GeCKO v2 Library Plasmid Production $1,150.00 $2,173.50
GeCKO v2 Library Virus Produciotn $1,650.00 $3,118.50
siRNA
Screening Services (single plate) $182.00 $343.98
Screening Services (human library) $10,925.00 $20,648.25
Screening Services (human subset - Genome) $6,050.00 $11,434.50
Screening Services (human subset - Drug Target) $3,375.00 $6,378.75
Screening Services (human subset - GPCR) $1.430.00 $2,702.70
Screening Services (human subset - protein kinase) $1,640.00 $3,099.60
Screening Services (human subset - Ubiquitin) $1,520.00 $2,872.80
Screening Services (human subset - Phosphatase) $1,300.00 $2,457.00
Screening Services (human subset - Protease) $1,475.00 $2,787.75
Screening Services (human subset - Ion Channnel) $1,410.00 $2,664.90
Screening Services (mouse library) $10,880.00 $20,563.20
Screening Services (mouse subset - Genome) $5,072.00 $9,586.08
Screening Services (mouse subset - Drug Target) $3,980.00 $7,522.20
Screening Services (mouse subset - GPCR) $1,475.00 $2,787.75
Screening Services (mouse subset - protein kinase) $1,635.00 $3,090.15
Screening Services (mouse subset - Ubiquitin) $1,500.00 $2,835.00
Screening Services (mouse subset - Phosphatase) $1,300.00 $2,457.00
Screening Services (mouse subset - Protease) $1,485.00 $2,806.65
Screening Services (mouse subset - Ion Channnel) $1,4109.00 $2,664.90
Screening Assay Services $48.00 $90.72
shRNA and cDNA - Glycerol stocks, Plasmids and Virus Production
Cherry Picked Clones (per sample, ≤ 6) $15.00 $28.35
Cherry Picked Clones (per set, 7 ≤ x ≤ 16) $98.00 $185.22
Cherry Picked Clones ((per sample, 17 ≤ x ≤ 48) $6 $11.34
Cherry Picked Clones (per plate ≤ 96) $294 $555.66
Sigma/SCRM Member Fee $2,730.00 $5,159.70
Cherry Picked Clones (per set, ≤ 16, Sigma/SCRM non-member) $280.00 $529.20
Cherry Picked Clones (per plate, Sigma/SCRM non-member) $840.00 $1,587.60
Sequence Verification of Clones (per plate) $552.00 $1,043.28
Relative OD600 (96 well plate) $8.00 $15.12
OD600 Pool (per source plate, 250ul - prerequisite: relative OD600) $30.00 $56.70
OD600 Pool (per source plate, 1000ul - prerequisite: relative OD600) $65.00 $122.85
Plasmid purification - miniprep (per set, ≤24) $96.00 $181.44
Plasmid purification - miniprep (per plate, ≤96) $370.00 $699.30
Plasmid purification - maxiprep (per sample, 1 ≤ x ≤ 16) $75.00 $141.75
Plasmid purification - maxiprep (per sample, 17 ≤ x ) $55.00 $103.95
Plasmid purification - maxiprep (per pool) $200.00 $378.00
Relative Picogreen (per plate, <96) $88.00 $166.32
Plasmid Quantization, and Normalization (per plate)Sigma/ $120.00 $226.80
Qubit dsDNA Measurement (per set, ≤ 6) $35.00 $66.15
Qubit dsDNA Measurement (per set, ≤ 24) $70.00 $132.30
Qubit dsDNA Measurement (per set, ≤ 96) $160.00 $302.40
Nanodrop DNA measurements (per sample, ≤ 42) $2.00 $3.78
Nanodrop DNA measurements (per plate, 96) $85.00 $160.65
DNA Pool (per source plate) - prerequisite: plasmid measurement) $600.00 $1,134.00
Lentivirus production (per set, 1 ≤ x ≤ 12) $600.00 $1,134.00
Lentivirus production (per set, 12 ≤ x ≤ 24) $1,000 $1,890.00
Lentivirus production (per set, 24 ≤ x ≤ 48) $1,600.00 $3,024.00
Lentivirus production (per set, 48 ≤ x ≤ 96) $2,400.00 $4,546.00
Retrovirus production (per set, 1 ≤ x ≤ 12) $840.00 $1,587.60
Retrovirus production (per set, 12 ≤ x ≤ 24) $1,400.00 $2,646.00
Retrovirus production (per set, 24 ≤ x ≤ 48) $2,240.00 $4,233.60
Retrovirus production (per set, 48 ≤ x ≤ 96) 3,360.00 $6,350.40
Equipment
Beckman Coulter Biomek FXP $132.00 $60.48
Hamilton Microlab STAR $32.00 $60.48
LI-COR Odyssey $10.00 $18.90
Molecular Devices ImagesXpress Micro $10.00 $18.90
Perkin Elmar EnVision $20.00 $37.80
Thermo Scientific Matrix WellMate Stacker $10.00 $18.90
Supplies and Labor
Biomek XP - 96 Well Transfer (per transfer) $10.00 $18.90
Biomek XP - 384 Well Transfer (per transfer) $36.00 $68.04
General Growth Media (100 ml) $5.00 $9.45
General Growth Media (500 ml) $15.00 $28.35
General Growth Media (1 l) $25.00 $47.25
Technical Labor $42.00 $79.38

External Rate = Internal's projected cost-per-unit, including overhead applied at 77% (e.g. 2016 approved indirect cost rate), plus a shared service management fee, equal to 5% of the per-unit-cost of each shared service.

* Based on Specific Grant or Contract
** iLab Users