PAN_GENEXP

PAN: Protein and Nucleic Acid Facility

» Gene Expression
& Bioanalyzer

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• Protocols
• Data Analysis
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Genomic Services

• Oligo Synthesis

• Gene Expression
& Bioanalyzer

• Real-Time PCR

• Pyrosequencing

• Next Gen Sequencing

• DNA Sequencing
& Fragment Analysis

Protein Services

• Protein Analytics

Located in rooms
B065 and B017

• OVERVIEW

** There are different types of service provided within the Gene Expression section. You must check the submission requirements for each service before placing your orders.

Full Service (Expression Analysis and Whole Genome DNA Analysis)
Hybridization and Scanning
Bioanalyzer QC

Full Service: (back to top)

• General Info. --

Investigators provide total RNA samples and PAN Facility carries out the entire target preparation, including Bioanalyzer QC of total RNA, then in vitro transcription, fragmentation, labeling, hybridization to the microarray, and scanning. The final raw data files are burned on the DVD. An e-mail notification is sent out upon the completion of the project. Turnaround time is usually 2 weeks, but exceptions apply.

Hybridization and Scanning : (back to top)

• General Info. --

Investigators provide fragmented and labeled targets, and PAN Facility carries out hybridization to the microarray indicated in the order, followed by the scan. Investigators are responsible for all QC prior to hybridization, including quality checks for total RNA and target fragmentation.

Bioanalyzer QC : (back to top)

• General Info. --

We do all sample QCs on our Agilent 2100 Bioanalyzers. The Agilent 2100 Bioanalyzer is a microfluidics-based platform, and with the lab-on-a-chip technology, it can provide sizing, quantification and quality control of DNA, RNA, proteins and cells in a short period of time. Each Agilent chip contains an interconnected set of microchannels that is used for separation of nucleic acid fragments or proteins based on their size as they are driven through it electronically.

§ Assays and their Applications --

PAN Facility currently offers different assays for a wide range of applications:

DNA Assays (DNA 1000 and High Sentivity DNA): provide sizing and quantification of DNA fragments and DNA smears down to pg/ul sensitivity.

RNA Assays:

Total RNA Assay (Eukaryote, Plant, Prokaryote)	provides RNA quality check with RIN (RNA Integrity Number), a quantification estimate and ribosomal ratios for total RNA and mRNA samples.
mRNA Assay	provides a quantitation estimate and percentage of rRNA contamination. No RIN provided.

Small RNA Assay: provides verification and optimization of miRNA after extraction procedures; analyzes miRNA directly in total RNA or in enriched samples; compares small RNA regions in extracts and tissues; separate miRNA from other small RNAs.

Please use the following table as a guide to choose the right assay for your samples. Before submitting your samples, you must also check out the concentration requirements for the assay chosen since each assay has different sensitivity level.

Starting Material

Sample Type

Assay Type

Size Analysis Range

* Sample Concentration
- Detection Range

DNA

dsDNA, cDNA, genomic DNA, NGS DNA

• DNA 1000

• High-Sensitivity DNA

25 - 1000 bp

50 - 7000 bp

1ng/ul-50ng/ul

5pg/ul-5ng/ul

RNA

Total RNA, mRNA, cRNA, fragmented RNA, microRNA

• Nano RNA (Eukaryote, Plant, Prokaryote)

• Pico RNA (Eukaryote, Plant, Prokaryote)

• Small RNA (6-150 nt)

25 - 4000 nt

6 - 150 nt

5ng/ul-500ng/ul

50pg/ul-10ng/ul

50pg/ul-2ng/ul

* Although the Bioanalyzer is capable of detecting the lowest concentration amounts shown, we would recommend to have your sample(s) in the higher detection range for better results.

• Data Release --

The data generated from the Agilent 2100 Bioanalyzer will be emailed to you in .pdf format and/or .xad format.

PDF file - contains run summary, assay details, electropherogram, gel image, result tables and the ladder info. The sample will be named as such, 'your initials'_'sample name'.
XAD file - is raw data file, which can be viewed using the free, downloadable Agilent 2100 Expert Software. This software allows you to manipulate the data at the regions of interest (specifically useful for DNA assays). For details about the sofware and what you can use it for, click here.

• Data Analysis --

Our data interpretation guide will help you understand your data better. For further analysis of your samples, you can use the Agilent 2100 Expert Software to open the raw (.xad) data file. If you still have questions/concerns regarding your data, please feel free to contact us at panbioanalyzer@stanford.edu.

• Turn-around Time --

Samples are usually processed within 24 hours and they will be disposed off after all successful runs. In case of any leftover and sample returned is requested, samples will be put back in freezer and kept for one week for you to come back and pick them up. After that, everything will be disposed of.