Sample Submission

Microarray Sample Submission Form

Genome Analyzer Sample Submisssion Form

We strive to provide you with data of the highest quality. The following are guidelines for sample submission in an effort to achieve this goal.  If you find that your samples do not meet the requirements, please contact our facility and a technician will work with you to establish what options are available.

We will not accept responsibility for ANY samples that fail due to inadequate concentration or quality.

Total RNA for Gene Expression Profiling

1. Total RNA of very high quality (28S:18S = 2:1, OD 260/280 > 1.8, OD 260/230 > 1.8) in DEPC-H2O is the best way to begin.
2. Samples should be cleaned with Qiagen Rneasy columns, including Trizol-isolated RNA. See protocols.  Samples for microRNA expression should be isolated and purified with Qiagen miRNeasy Mini kit (cat. no. 217004).
3. Dnase-treatment is highly recommended as RNeasy columns alone may not completely remove genomic DNA. See protocols.
4. Total RNA isolated from whole blood needs to be globin-reduced.  We recommend Ambion GLOBINclear kit (cat. no. AM1980, AM1981).
5. Samples that need to be concentrated at our facility will be assessed an additional fee.
6. Illumina expression samples should be batched to match the capacity of each microarray. For example, the Hu6 array will accomodate 6 samples.

platform	assay	min. amount	min. conc. in H2O
affymetrix	IVT express	> 3 ug	> 75 ng/ul
affymetrix	expression (3'-standard)	> 6 ug	> 0.5 ug/ul
affymetrix	2-cycle expression	> 2 ug	> 50 ng/ul
affymetrix	exon	> 4 ug	> 750 ng/ul
affymetrix	gene array	> 2 ug	> 150 ng/ul
exiqon	miRNA expression	> 200 ng	> 50 ng/ul
illumina	expression	> 3 ug	> 75 ng/ul
illumina	expression hyb only	> 1.5 ug cRNA	> 150 ng/ul
illumina	microrna expression	> 2 ug	> 150 ng/ul
illumina	dasl	> 2 ug	> 150 ng/ul
nimblegen	expression	> 10 ug	> 1 ug/ul
nimblegen	expression hyb only	> 13 ug	> 1 ug/ul
spotted	expression	> 2 ug	> 0.5 ug/ul
spotted	expression hyb only	please inquire	> 0.5 ug/ul

We will not accept responsibility for ANY samples that fail due to inadequate concentration or quality.

Genomic DNA for SNP Genotyping

1. Genomic DNA concentrations should be the same for all samples, especially if considering CNV analysis.
2. Genomic DNA must be run on an agarose gel (e.g. 150 ng/sample on a 1% gel). Samples should not have fragments that run below 2 kb. If a gel cannot be run, a note of permission to process without gel image should be included with the sample submission. We will not accept responsibility for ANY samples that fail due to inadequate concentration or quality.
3. NanoDrop readings of genomic DNA may not be as accurate as larger volume spectrophotometers. If using a fluorometer, samples submitted for Illumina processing should be 50-60 ng/ul.
4. Genomic DNA for Affymetrix assays should be diluted in reduced TE buffer (10 mM Tris, 1mM EDTA, pH 8.0). All other assays, e.g. Illumina, should use TE buffer (10 mM Tris, 1mM EDTA, pH 8.0).
5. Illumina projects: Genomic DNA should be submitted in 96-well plates.  All samples should be at the same concentration (70 ng/ul).  Samples need to be submitted in multiples of 16 (e.g. 16, 32, etc.) for efficient reagent consumption. If submitting in a 96-well plate, PLEASE load samples in columns (vertically) as opposed to across the plate (rows/horizontally).  Please provide an electronic file with sample identities and plate coordinates.
6. Sequenom projects: Genomic DNA can be submitted in either 1.5 ml microfuge tubes or 96-well plates.  If submitting in a 96-well plate, PLEASE load samples in rows (horizontally) and leave 2 wells blank.  This removes complexity involved in assembling the amplification plate.  Please provide an electronic file with sample identities and plate coordinates.
7. Sequenom SNP submission: “rs” numbers should in a single column in excel or text (.txt) format.

platform	assay	min. amount	min. conc.
affymetrix	6.0	> 2 ug	= 60 ng/ul
illumina	infinium II & HD (e.g. 610Q, 1M DUO, OMNIquad)	> 2 ug	= 70 ng/ul
illumina	infinium methylation beadchip	> 700 ng	= 70 ng/ul
illumina	golden gate	> 1 ug	= 70 ng/ul
nimblegen	genotyping	> 2.5 ug	> 1 ug/ul
nimblegen	genotyping hyb only	> 13 ug	> 1 ug/ul
sequenom	genotyping	> 200 ng	> 10 ng/ul

Sending Samples for Processing

1. Please complete the sample submission form with purchase order number and enclose with your samples.
2. Please ship samples overnight on dry ice to: Shrikant Mane, Keck Facility Microarray Resource, 300 George Street, Rm#2110, New Haven, CT 06511, 203-785-7869.
3. It is the responsibility of the user to collect any unused sample from us within 60 days of receiving the data.  Samples will be discarded without notice after this timeframe.
4. Unsure about something?  Please contact microarrays@yale.edu or call 203-785-7869.