University of Idaho - IBEST
DNA Sequencing Analysis Core and Microarray Core
Nimblegen Microarray Sample Submission
July 6, 2011 - Version 1.2
The University of Idaho – IBEST DNA Sequencing Analysis Core and Microarray Core
wishes to work with investigators to ensure they receive good data and the correct
data to answer the biological questions intended for the project. As such, core
personnel request that investigators:
1. Consult a core bioinformatician as to the projects goals, design, and replication
as early as possible in the project (preferably before sample collection).
2. Consult a core molecular specialist during sample preparation in order to
ensure optimal quality data.
Contact:
Bioinformatics: Matt Settles 1-208-885-6051
Laboratory: Suresh Iyer and Dan New 1-208-885-7023
Submitting Samples to the IBEST Microarray Core
Documentation
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ALL samples (in tubes) needs to be accompanied by a completely labeled gel/Bioanalyzer
report (e.g. 1, 2, 3) and ladder
◦ Gels should be high quality regarding camera resolution, band intensity, band separation,
ladder separation, and sufficient quantity of nucleic acid.
◦ Laser printer copies do not provide the resolution needed.
◦ Each resolute band of each ladder (per gel) should be clearly labeled on the gel image.
◦ Each sample should be clearly labeled both on the gel image and in the tube 1-99 (e.g. 1,
2, 3).
A completed "microarray sample submission sheet" (provided) is also required, both email and
physical copy accompanying the samples.
Shipping
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Please ship samples overnight by FedEx on dry-ice to
C/O Daniel New
C/O Matt Settles
Biological Sciences
IBEST DNA Sequencing Analysis Core
Life Sciences South Rm 252
University of Idaho
Moscow, ID 83844
All samples must be accompanied by a complete physical “microarray sample submission
sheet”.
Below is a guide to quantity and quality by common microarray types, if there are
any questions, or you have an uncommon sample type please call the core.
Expression Microarrays
High quality RNA is required for optimal cDNA yield and cDNA labeling for microarray hybridization.
RNA can be extracted using the RNA extraction method of your choice and followed by DNAse
treatment prior to submission (we recommend the Ambion Turbo-DNA-free kit). Submit samples in
1.5ml tubes where sample volume allows.
RNA – Submission
Array Format
Eukaryotes
Prokaryotes
All Array Types
10µg total RNA
10µg total RNA
1µg poly-A+ RNA
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The following values are post DNAse Treatment and as quantified by Nanodrop.
Should you not be able to achieve the necessary sample quantity, we recommend the
Sigma Transplex complete whole transcriptome amplification kit (WTA2)
Spectrographic QC of RNA (Nanodrop) (Highly Recommended)
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RNA concentration ≥1.11µg/µL (A260 x 40 x Dilution Factor)
A260/A280 ≥ 1.8
A260/A230 ≥ 1.8
Agarose Gel and/or Bioanalyzer QC of RNA
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Verify RNA samples are of sufficient molecular weight
Samples are not degraded.
Contain no genomic contamination
Bioanalyzer: Recommended
 RIN (RNA Integrity Numbers via Bioanalyzer) ≥ 6.0
 28s/18s ≥ 1.5
cDNA – Submission
Array Format
Eukaryotes
Prokaryotes
All Array Types
2µg total cDNA (1µg minimum)
10µg total cDNA
* As quantified by Nanodrop
Spectrographic QC of cDNA (Nanodrop) (Highly Recommended)
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RNA concentration ≥ 25ng/µL (A260 x 50 x Dilution Factor)
A260/A280 ≥ 1.8
A260/A230 ≥ 1.8
Agarose Gel QC of cDNA
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Verify cDNA samples have an average fragment size ≥ 400bp
Above RNA requirements apply; please provide core personnel with RNA quantity and QC
information prior to cDNA synthesis for comment.
ChIP-chip and MeDIP Microarrays
High Quality DNA (IP/MeDIP or Input) is required to obtain optimally labeled samples for array
hybridization. Samples should be delivered in nuclease-free water or 1X TE buffer (10 mM Tris-HCl
and 0.1 mM #DTA, pH 7.5-8.0) and sheared such that a significant majority of the DNA is ≥ 200
nucleotides in size.
IP/Input – Submission
Array Format
IP/MeDIP sample
Input
1x385K array
1.5µg
1.5µg
4x72K array
1.5µg
1.5µg
1x2.1M array
3.5µg
3.5µg
3x720K array
1.5µg
1.5µg
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As quantified by Nanodrop.
Should you not be able to achieve the necessary sample quantity, we recommend the
Sigma Transplex complete whole genome amplification kit (WGA2)
Spectrographic QC of DNA (Nanodrop) (Highly Recommended)
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DNA concentration ≥18.75ng/µL (43.75ng/µL – 1x2.1M array) (A260 x 50 x Dilution Factor)
A260/A280 ≥ 1.7
A260/A230 ≥ 1.6
Agarose Gel and/or Bioanalyzer QC of DNA
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Verify DNA samples are of sufficient molecular weight
Samples are not degraded.
CGH and CNV Microarrays
Purified, unamplified, and unfragmented genomic DNA (gDNA) is required to obtain optimally labeled
samples for array hybridization. Samples should be delivered in nuclease-free water or 1X TE buffer
(10 mM Tris-HCl and 0.1 mM #DTA, pH 7.5-8.0.
gDNA – Submission
Array Format
gDNA
1x385K array
1.5µg
4x72K array
1.5µg
1x2.1M array
2.5µg
3x720K array
1.5µg
12x135K array
1.5µg
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As quantified by Nanodrop.
Spectrographic QC of DNA (Nanodrop) (Highly Recommended)
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DNA concentration ≥ 18.75ng/µL (31.25ng/µL for a 1x2.1M array) (A260 x 50 x Dilution Factor)
A260/A280 ≥ 1.8
A260/A230 ≥ 1.9
Agarose Gel and/or Bioanalyzer QC of DNA
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Verify RNA samples are of sufficient molecular weight and samples are not degraded.