PAN_GENEXP

PAN: Protein and Nucleic Acid Facility

» Gene Expression
& Bioanalyzer

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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

• SUBMISSION REQUIREMENTS

** There are different types of service provided within the Gene Expression section. Please check for the appropriate sample submission requirement for each service before placing your orders.

Full Service
Hybridization and Scanning
Agilent Bioanalyzer QC

FULL SERVICE (Back to top)

High quality total RNA* is processed according to the appropriate protocol, the targets are hybridized to the Affymetrix array, and the array is scanned. The resulting data files are put on a CD or uploaded to the customer’s server upon request.
*All samples are checked on Agilent Bioanalyzer and Nanodrop before processing.

Type of array	Starting material	Assay	*Amount of starting material required for one* sample**
3’ Expression*	Total RNA	3’IVT Express Ambion MesageAmp II	50-500ng 20-500ng
Gene 1.0ST	Total RNA	Ambion WT Expression followed by Affymetrix GeneChip WT Terminal Labeling kit	50-500ng
Exon	Total RNA	Ambion WT Expression followed by Affymetrix GeneChip WT Terminal Labeling kit	50-500ng
Tiling Promoter	Total RNA	Affymetrix GeneChip WT Double-Stranded Target or Chromatin Immunoprecipitation	3ug-5ug
miRNA	miRNA	GeniSphere 3DNA FlashTag Biotin HSR	100-1000ng
Human SNP 6.0	ds DNA	Affymetrix Genome-Wide Human SNP Nsp/Sty 6.0	500ng-1ug (50ng/uL)

* The assay for 3’Expression arrays will be chosen based on the available RNA quantity.

HYBRIDIZATION AND SCANNING (Back to top)

Fragmented and labeled targets are hybridized to the Affymetrix array using the appropriate hybridization mix. After the array is scanned, the resulting data files are put on CD or are uploaded onto customer’s server upon request.

Type of array	Hybridization target	Target concentration
3’ Expression	Biotin-labeled, fragmented cRNA	49/64 array format: 15ug in 40ul* 100 array format (Midi): 12ug in 30ul 169 array format (Mini): 7.5ug in 20ul
Gene 1.0ST	Biotin-labeled, fragmented single stranded DNA	~27ul**
Exon	Biotin-labeled, fragmented single stranded DNA	~60ul**
Tiling Promoter	Biotin-labeled, fragmented double stranded DNA	~7.5ug (~60uL)***
miRNA	GeniSphere 3DNA FlashTag Biotin HSR	21 ul
Human SNP 6.0 array	Biotin-labeled, fragmented double stranded DNA	~73uL

* If using Affymetrix 3’IVT Express protocol
** If using Affymetrix GeneChip WT Terminal Labeling protocol
***If using Affymetrix GeneChip WT Double-Stranded Target protocol

AGILENT BIOANALYZER QC (Back to top)

Samples are analyzed on Agilent 2100 Bioanalyzer. The resulting pdf report (and .xad file if necessary) is e-mailed to the customer.

Submit your samples in 3ul of appropriate concentration range.
Label each tube clearly as such: Customer initials_ last 3 digits of the Run number a shown on the order confirmation.
Drop off the samples in the PAN freezer, include order form
Please provide only 3ul aliquots, NOT your entire sample. The samples will be disposed off after all successful runs. In case the sample needs to be analyzed again due to chip or technical error, we will keep the sample until the successful result is obtained.

**NOTE** Samples are usually processed within 24 hours. For customers who want to have the leftover of their samples back afterward, please come down to PAN to pick them up. We will save them in the same freezer and in the back racks for one week. After that, everything will be disposed of.

Please refer to the table below to decide which assay fits you best.

Assay type	Size range	Quantitative range*
RNA 6000 Nano (eukaryote, prokaryote, or plant)	25-4000 nt	25ng/ul - 500 ng/ul
RNA 6000 Pico (eukaryote, prokaryote, or plant)	25-4000 nt	Less than 25ng/ul
Small RNA	6-150 nt	50pg/ul - 5ng/ul
DNA 1000	25-1000 nt	10ng/ul - 50ng/ul
High Sensitivity DNA	50-7000 nt	50pg/ul - 10ng/ul

* Although Agilent Bioanalyzer is capable of detecting the lowest concentration amounts shown, we recommend that, for best results, customers provide samples with concentrations closer to the higher detection range.

* Agilent website provides free Data Evaluation software available for download. This software can be used if data manipulation is needed. Upon customer’s request, we will e-mail the .xad file that can be viewed and re-analyzed using the software.