Genomics - Microarray/Q-PCR (La Jolla)

Overview

The facility provides full-service microarray-based global analysis of gene expression in RNA samples from humans or mice, using an Illumina platform. Starting with investigator-provided RNA samples, the facility confirms RNA quality, and then performs microarray analysis as well as initial data analysis. Array data are returned to the investigator, and if desired, also passed on to the Informatics and Data Management core facility for more detailed analysis. The full-service Quantitative real-time PCR (Q-PCR) service starts with RNA, and then provides either one or two-step Q-PCR analysis, utilizing primers from investigators or designing and obtaining custom primers. Q-PCR analysis is predominantly SYBR green-based analysis, but hybridization probe (e.g. TaqMan) approaches are also supported. The core provides control primers and assists with experimental design, as well as providing basic relative quantitation analysis. Q-PCR-based analysis in the facility can also provide gene, RNA, or viral copy number data.
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Services

  • RNA sample quantity and quality analysis
  • Microarray analysis: from total RNA to global mRNA expression data. A typical analysis starts with 100 - 500ng of total RNA, but analysis is possible down to 500pg of RNA utilizing a double amplification protocol.
  • The core provides initial microarray data analysis including Sample_Probe Profile, Sample_Gene profile and list of genes with 2 folds differences. Additional more advanced informatic analysis is available through the Bioinformatics core facility.
  • Q-PCR service: starting from total RNA to data analysis – either one step RT-qPCR from RNA, or two step Q-PCR first synthesizing cDNA.
  • Q-PCR analysis using SYBR Green or TaqMan methods.
  • If desired, the core will design and purchase gene-specific primers for SYBR Green analysis – i.e., one can go from RNA sample and gene accession numbers to quantitative expression data.
  • PCR or Q-PCR-based analysis of DNA from transgenic mice, starting with tail samples.
  • Typically, analysis is relative quantitation, but absolute quantitation is also available.
  • Special services: RNA purification, Copy Number Variation (CNV) Analysis Using TaqMan® Assays.

Equipment and Resources

  • MicroArray: Illumina BeadStation microarray system
  • Roche LC480 real time QPCR instrument (interchangeable 96 or 384 well)
  • Stratagene Mx3000p real-time QPCR instrument (96 well)
  • ABI 7900 real time QPCR instrument (interchangeable 96 or 384 well)
  • BioRad Experion (BioAnalyzer equivalent)
  • Nanodrop Spectrophotometer

Contact

Kang Liu, Ph.D., Core Manager


Jian Xing, B.S., QPCR Associate


Craig Hauser, Ph.D., Scientific Director

Price List

Microarray
cRNA Amplification for Microarrayssample$70.00$87.50$94.50$183.40L550
Full Illumina Microarray service, from total RNA to text files (per genome, chip not included)sample$130.00$162.50$175.50$340.60L552
Full Illumina Microarray service, from total RNA to text files (per genome, chip not included), 2-round amplificationsample$230.00$287.50$310.50$602.60L548
Human HT-12 48K Array ,whole chipchip$980.00$980.00$1,323.00$1,323.00L566
Human HT-12 48K Array, per genomegenome$81.67$81.67$110.25$110.25L568
Illumina beadchip mouse 6x2, whole chipchip$1,034.00$1,034.00$1,395.90$1,395.90L563
Illumina beadchip mouse 8x1, whole chipchip$862.00$862.00$1,163.70$1,163.70L564
Illumina service, pre-labeled cRNA to text files (per genome, chip not included)sample$60.00$75.00$81.00$157.20L560
Mouse 6 48K array, per genomegenome$172.33$172.33$232.65$232.65L558
Mouse Ref 8 24K array, per genomegenome$107.75$107.75$145.46$145.46L555

QPCR
Additional Consulting or Traininghour$50.00$62.50$67.50$131.00L607
Bulk Q-PCR analysis (48 samples or more)reaction$2.00$2.50$2.70$5.24L615
cDNA Synthesis reactionreaction$12.00$15.00$16.20$31.44L606
Miscellaneouseach$1$1$1$1L131
Q-PCR analysis from cDNA, per reaction (2-step, SYBR or Taqman)reaction$2.50$3.13$3.38$6.55L605
RNA Intergrity check (12 samples/run, up to 12 samples)run$60.00$75.00$81.00$157.20L611
RNA Purification from Cellssample$12.00$15.00$16.20$31.44L609
RNA Purification from Tissuessample$18.00$22.50$24.30$47.16L610
SYBR Green Primer design and test (2 pairs, guarantee to work or no charge)set$60.00$75.00$81.00$157.20L601
Taqman Primer/Probe design and validation (primers and probe included)setinquireinquireinquireinquireL608
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