This Laboratory performs a research and service function for the entire UCLA campus and beyond. Mass spectrometry has become an indispensable tool in biological research because in a qualitative mode it allows unequivocal identification of a wide range of compounds including small (lipids, amino acids, bases, carbohydrates etc) and large (proteins and nucleic acids) molecules from impure samples. In a quantitative mode the measurements can be extra-ordinarily precise. Mass spectrometry is having an increasingly important impact in all areas of biochemistry, but most notably in the detailed characterization of the proteome, and now the metabolome, that have emerged as the successors to the Human Genome Project. While our research has previously been broadly defined within the context of cellular communication, with time has come increasing involvement in other research projects. This was not unexpected and in fact is welcomed because significant expense and effort is required not only to purchase, but to also sustain and operate these complex instruments, and it is not appropriate for all laboratories to have their own instruments. The services that are provided include analyses by combined gas chromatography/mass spectrometry, combined liquid chromatography/mass spectrometry, and the expertise and experience that is necessary to use these techniques to answer questions related to biochemistry, and interpret the data.

More information at http://massspec.chem.ucla.edu

The facility offers DNA extractions from whole blood and other tissue types, and storage of extracted DNA. We use the Autopure LS™ nucleic acid purification instrument from Gentra Systems for extracting DNA. This instrument provides a highly automated process with very high quality DNA, samples are quantitated using OD 260/280. Once DNA has been obtained from the provided sample, it can be returned immediately or stored in -20°C freezer for future use. We'll also aliquot DNA at the desired concentrations. DNA can be stored indefinitely within BSPC. All samples are logged in our database and are bar-coded with our sample number and customer's identification code.

We will soon initiate RNA extraction.

Sample Handling at the Facility

All samples are entered into a database that gives each entry an ID number for sample handling and data storage purposes.

Sample Type and Amount required

Blood (fresh whole blood): 1-10mL; cultured lymphoblast cell lines (fresh): 20-50 million cells count; buccal mouthwash (fresh): in 10-20mL mouthwash; clotted blood: 1-10mL; tissues (frozen or fresh): 100-300mg.

Please check with BSPC for any new sample type and other sample size availability.

Service Type and Cost

Autopure (AP) extraction on blood - $25/extraction
Autopure (AP) extraction on buccal mouthwash - $25/extraction
Manual extraction on clotted blood - $36/extraction
DNA dilution or aliquote preparation - $2/tube of dilution or aliquot
DNA plating (96 DNA dilution on 96-well plate) - $220/96-well plate
DNA storage (for DNA samples not extracted BSPC) - $1/tube of DNA sample

An account will be set up for each P.I. using the facility. Customers must bring a signed Recharge Order Request (P39) prior to receiving services.

Facility Hours

Monday through Friday: 9:00 am to 5:00 pm, Saturday and Sunday: closed

Sample Drop-off Hours

Monday through Thurs: 9:00am to 5:00pm, Friday and the weekday before holiday: 9:00am to 3:00pm.

Contact Info:

Address

UCLA, Gonda Center, BSPC Room 4310, 695 Charles E. Young Drive South, Los Angeles, CA 90095-7088. Phone 310- 267 2715, Fax 310-794 9613

(Number 53 on the UCLA Map )

Director

Nelson B. Freimer, Prof., Email: nfreimer@mednet.ucla.edu

Phone: 310-794 9571, Room: 3506A Gonda Center

Manager

Eva Oi-Wa Choi, Email: ochoi@mednet.ucla.edu

Phone: 310- 267 2715, Room: 4310 Gonda Center

Billing

Margaret Chu, Admin Analyst, Email: mchu@mednet.ucla.edu

Phone: 310-794 9576, Room 3506 Gonda Center

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The SCGC operates an Illumina BeadLab 1000, a LIMS supported laboratory system capable of processing custom snp, whole genome snp genotyping, methylation profiling as well as custom and whole genome gene expression profiling.
In support of our methylation services the SCGC has recently invested in an iScan scanner, aotuloader, additional Tecan robotics and a SciGene little dipper array processing robotic workstation. These capital improvements have resulted in a greatly increased methylation  chip processing capacity as well as increased reproducibility and consistency. The facility is capable of running all current Illumina products designed for the BeadArray or iScan readers and can process up to 576 whole genome methylation samples per day.

Illumina whole genome methylation profiling protocols begin with 500ng to 1ug of genomic DNA isolated from whole blood or tissue. All samples are quanted using a Picoogreen fluorescent assay and normalized to 50 ng/ul prior to Bisulfite conversion . Bisulfite conversion is accomplished using the Zymo EZ kit protocol and reagents. Converted DNA then proceeds into Illumina Infinium whole genome genotyping protocol and ultimately is hybridized to Methylation -27 chips, which are read on the iScan reader. The protocol takes 4 days to complete.  Beta( methylation ) values are reported in flat file format suitable for analysis in many 3rd party applications. Copies of the GenomeStudio( Illumina) project and raw data are also made available.

The SCGC currently supports all Illumina methylation products including Human Methylation -27 chips GoldenGate custom methylation assays.

The SCGC operates an Illumina BeadLab 1000, a LIMS supported laboratory system capable of processing custom snp, whole genome snp genotyping, methylation profiling as well as custom and whole genome gene expression profiling.

In support of our gene expression services the SCGC has recently invested in an iScan scanner, additional Tecan robotics and a SciGene little dipper array processing robotic workstation. These capital improvements have resulted in a greatly increased expression chip processing capacity as well as increased reproducibility and consistency. The facility is capable of running all current Illumina products designed for the BeadArray or iScan readers and can process up to 288 expression samples per day.

Illumina whole genome gene expression profiling protocols begin with 100 ng  of total  RNA isolated from whole blood or tissue. All samples are quanted using a Ribogreen fluorescent assay and normalized to 10 ng/ul prior to amplification. Amplified and labeled cRNA is produced using the Illumina specific Ambion TotalPrep kit. 1st and 2nd strand cDNA is produced using the Ambion kit and purified using a robotic assisted magnetic capture step. Biotinylated cRNA is produced from the cDNA template in a reverse transcription reaction. Typical yields are in excess of 1.5 ug.  After a second Ribogreen quant and normalization step, amplified and labeled cRNA is  hybridized overnight at 58C to the expression arrays. Hybridization is followed by washing, blocking, staining and drying on the Little Dipper processor. Array chips are scanned on either the Beadarray reader or the iScan reader. Expression data is extracted and compiled using BeadStudio software ( Illumina) and extracted( un-normalized) data as well as raw scan data is delivered to end users on DVD
The SCGC currently supports all Illumina gene expression whole genome products including Human and Mouse Ref6 and Ref8 chips, RatRef12 and Human HT-12 chips. In addition we support DASL and GoldenGate custom expression profiling.