DNA Sample Submission

 

Table of Contents

Biosafety

DNA Amount Requirements

DNA Quality Requirements

ChIP Quality Assessment

DNA Sample Shipment

Preparing DNA for Shipping

Shipping on Dry Ice

Sample Receipt Confirmation

Disclaimer for Low Sample Amount/Quality

DNA sample amount and quality are essential for good data quality and key to the project success. Customer should assess the DNA amount and quality before submitting the samples. Arraystar will always perform sample QC upon sample receipt. The sample QC assessment at Arraystar is final. Should there be issues about the amount or quality, we will contact you immediately for you to decide whether to replace, proceed, or drop the sample from the study.

 

For (hydroxy)MeDIP project, Customer should submit purified, intact genomic DNA samples as the starting materials.

 

For ChIP project, Customer should perform chromatin immunoprecipitation and ChIP enrichment QC. The above procedures are not available as a service from Arraystar. Both “IP” and “Input” DNAs are submitted as the starting materials. “Mock” DNA by non-immune IgG is required as part of the ChIP quality assessment by qPCR. Mock DNA sequencing as a background control is optional. It could be better than Input only when a sufficient amount of the Mock DNA is recovered.

 

Biosafety

 

If your DNA samples were extracted from any biohazardous sources, you must disclose before placing your order and shipping your samples. Any infectious agents must be inactivated either during DNA purification procedure or by a specific inactivation method. You must ensure your materials and the shipment free of any contamination risk, including the packaging from inside out. We will evaluate and determine the biosafety compliance and acceptance of the samples.

 

DNA Amount Requirements

 

Recommended DNA Amount per Sample
DRIPc-sequencing	>10ug genomic DNA extracted •   By Qiagen DNeasy or QiaAMP DNA Kits. DO NOT use RNase in the procedure.
eccDNA Sequencing	1*- 3 ug genomic DNA
(h)MeDIP-chip/sequencing/qPCR	2*- 5 ug genomic DNA
ChIP-chip/sequencing/qPCR, ChIP performed by customer	20*- 40 ng IP-enriched DNA 200 ng sonicated input DNA 20*- 40 ng mock IP-enriched DNA (optional)

*The recommended minimum amount for each sample is intended for use in the entire experiment for a single attempt, including sample QC. It is recommended to supply twice the recommended minimum amount to avoid project delays.

If the recommended minimum amount is not obtainable, please consult our technical support by email at support@arraystar.com to make special arrangements.

 

DNA Quality Requirements

 

Genomic DNA Quality
Purification method	•   By Qiagen DNeasy Kits •   By most genomic DNA isolation kits.
Solution	Molecular biology grade water precipitation method.
DNA concentration	≥ 20 ng/uL by Nanodrop. Too low a value may be inaccurate for Nanodrop measurement. RNA contamination removal by, e.g. RNase treatment. Contaminant RNA can cause overestimation of the DNA concentration/amount.
Purity by OD260/280	> 1.7 by Nanodrop. A low value may indicate protein contamination.
Purity by OD260/230	> 1.8 by Nanodrop. A low value may indicate organics contamination.
DNA integrity	By gel electrophoresis as a predominant high molecular weight DNA band.

 

ChIP-enriched DNA Quality
DNA fragment size range	200 ~ 1000 bp
Solution	Molecular biology grade water
DNA concentration	By fluorometer, e.g. Qubit (Thermo Fisher). NanoDrop reading becomes unreliable when the concentration is very low.
ChIP enrichment QC	By qPCR, to evaluate the enrichment efficiency and the background. See “ChIP quality assessment” below.

 

ChIP Quality Assessment

 

For (hydroxy)MeDIP project, Arraystar will perform (h)MeDIP, which includes MeDIP enrichment quality assessment.

For ChIP project, Customer performs the ChIP as well as ChIP enrichment QC. Please QC the ChIP quality before submitting the samples, as Arraystar cannot be responsible for ChIP performed by customer.

1. Setup qPCR assay for ChIP quality

	IP	Input	Mock
qPCR Mix	1X	1X	1X
DNA volume	1 uL	1 uL	1 uL
Positive control primer set*	0.2 uM	0.2 uM	0.2 uM

* qPCR Primers design is based on a selected previously known specific binding site for your chromatin binding factor.

2. ChIP-qPCR Data Analysis (ΔΔCt method)

a)      Normalize each DNA Ct value to the Input DNA Ct value for the same qPCR assay (Ct) to account for chromatin sample preparation variation.

         ΔCt[normalized] = Ct - Ct[Input]

         Calculate %Input for each DNA fraction:

         %input = 2^Ct[Input]-Ct X Fd X 100%

         Where Fd is the Input dilution factor. For example, if 20 uL sonicated DNA is used as Input and 100 uL is used for IP (eluted in 20 uL), then Fd(IP)=1/5.

b)      Subtract the normalized ChIP Ct value for the normalized background (mock IP) Ct value.

         ΔΔCt[Chip/Mock] = ΔCt[normalized Chip] - ΔCt[normalized Mock]

3. Assessment of ChIP quality

a)      Input Ct value should be less than 30, to ensure sufficient Input was used.

b)      %Input for Mock should be less than 0.01%, to ensure low background.

c)      IP Ct value should be at least one cycle less than Mock Ct value to be considered quantitatively significant above the background noise. i.e. Ct[mock] – Ct[ChIP] > 1.0

 

DNA Sample Shipment

 

Please complete, sign, and email us a Project Form prior to sending your samples.

The sample package shall be shipped to the address:

ATTN: Samples Receiving (Project#______ ) Arraystar Inc. 9430 Key West Avenue #128 Rockville, MD 20850 USA Tel: 888-416-6343

 

Preparing DNA for Shipping

1)      Dissolve the DNA in water or TE buffer.

2)      The DNA can be stored at -80°C or -20°C.

 

Shipping on Dry Ice

•         Use nuclease-free certified, 1.5 mL capacity, screw-cap microtubes;

•         Seal the cap with Parafilm strip;

•         Place the sample tubes in a plastic bag;

•         Use 10 kg dry ice as refrigerant (sufficient for both domestic and international);

•         Include a copy of the signed Project Form in a waterproof bag, separate from your samples;

•         Check the carrier for dry ice/international shipping requirements;

•         If possible, avoid a drop-off date with coming weekends, holidays, such as Thursday or Friday;

•         Obtain the tracking number and notify by email the Arraystar representative who is working with you for the project.

 

Sample Receipt Confirmation

All shipments and inquiries should reference the Project Number assigned to your project by Arraystar. You will receive notification from us upon receipt of your samples. We'll notify you if there are any discrepancies between your Sample Submission Form and the contents we receive, or if there are any issues with the physical condition of the samples.

 

Disclaimer for Low Sample Amount/Quality

 

For the best results, the DNA samples must meet the amount and quality requirements. In case of low sample amount or quality, we will contact you for you to decide whether to replace, proceed, or drop the sample from the study. With your consent and approval, it is possible for us to proceed with the experiment. In such a case, you understand the data quality and the success rate may decrease progressively with the lowered sample amount or quality. Although usable data may still be obtainable, we cannot predict for certainty nor do we guarantee the quality and success rate of the data outcomes.