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Sample Preparation & Shipping

This document provides guidelines on how to prepare, quantify, and submit samples to Novogene. Whether you are submitting DNA or RNA samples, it is essential that the appropriate instructions be followed to enable the successful completion of your project.

Sample Requirements
Pre-Quality Control (QC) Instructions
Demonstrations of Qualified DNA/RNA Samples
Sample Labeling Recommendations
Sample Packing Recommendations
Completing the Sample Submission Form
Shipping Samples to Novogene

Sample Requirements

Sample quality directly impacts sequencing quality and subsequent bioinformatics analysis. Therefore, Novogene has extensive sample quality control procedures to ensure submitted samples conform to requirements for downstream processing.

To guarantee the normal processing of your project, samples should meet the standards given below. If your samples do not meet these standards, and you are unable to produce higher-quality samples, please consult with your Novogene Project Manager before shipping your samples.

Notes:

  • Input quantity should be determined by Qubit® instead of by NanoDropTM, and the final quantity and concentration should conform to Novogene’s specifications.
  • Samples not meeting these specifications should be designated as “at risk” by the customer, and will be subject to billing regardless of data quality. Please consult the Project Manager for further details.

1. Human Whole Genome/Exome Sequencing

Library Type Sample Type Amount (Qubit®) Volume Concentration Purity
(NanoDropTM/agarose gel)
Strongly recommended Required
Human Whole Genome/ Exome Sequencing Genomic DNA ≥ 2 μg ≥ 1 μg ≥ 20 μL ≥ 50 ng/μL OD260/280 = 1.8 – 2.0,

no degradation, no contamination

PCR products of

single-cell whole genome

≥ 2 μg ≥ 1 μg ≥ 20 μL ≥ 50 ng/μL Fragments should be longer than 500 bp
FFPE* ≥ 3 μg ≥ 1.5 μg Fragments should be longer than 1500 bp

* formalin-fixed, paraffin-embedded

2. Target Region Sequencing

Library Type Sample Type Amount (Qubit®) Volume Concentration Purity
(NanoDropTM/agarose gel)
Strongly recommended Required
Target Region Capture Genomic DNA ≥ 1 μg ≥ 500 ng ≥ 20 μL ≥ 50 ng/μL OD260/280 = 1.8 – 2.0,

no degradation, no contamination

PCR products of single-cell whole genome ≥ 1 μg ≥ 500 ng ≥ 20 μL ≥ 50 ng/μL Fragments should be longer than 500 bp
FFPE ≥ 2 μg ≥ 1 μg Fragments should be longer than 1500 bp

3. Plant & Animal Genome Sequencing

Library Type Sample Type Amount (Qubit®) Volume Concentration Purity
(NanoDropTM/agarose gel)
Strongly recommended Required
≤ 500 bp Insert Genomic DNA ≥ 1.4 μg ≥ 700 ng ≥ 20 μL ≥ 50 ng/μL OD260/280 = 1.8 – 2.0,

no degradation,

no contamination

Mitochondrion/ Chloroplast DNA ≥ 1.6 μg ≥ 800 ng ≥ 20 μL ≥ 50 ng/μL
Genotyping by Sequencing Genomic DNA ≥ 500 ng ≥ 300 ng ≥ 10 μL ≥ 50 ng/μL
2 Kb Insert Genomic DNA ≥ 30 μg ≥ 15 μg ≥ 20 μL ≥ 50 ng/μL
5 Kb Insert Genomic DNA ≥ 30 μg ≥ 15 μg ≥ 20 μL ≥ 50 ng/μL
10 Kb Insert Genomic DNA ≥ 50 μg ≥ 25 μg ≥ 20 μL ≥ 50 ng/μL
> 10 Kb Insert Genomic DNA ≥ 80 μg ≥ 40 μg ≥ 20 μL ≥ 50 ng/μL

4. Microbial Genome Sequencing

Library Type Sample Type Amount (Qubit®) Volume Concentration Purity

(NanoDropTM/agarose gel)

Strongly recommended Required
≤ 500 bp Insert Genomic DNA ≥ 1.6 μg ≥ 800 ng ≥ 20 μL ≥ 50 ng/μL OD260/280 = 1.8 – 2.0,

no degradation, no contamination

Meta Library Genomic DNA ≥ 1.6 μg ≥ 800 ng ≥ 20 μL ≥ 50 ng/μL Fragments should be longer than 500 bp
PCR-Free Library Genomic DNA ≥ 10 μg ≥ 5 μg ≥ 20 μL ≥ 50 ng/μL OD260/280 = 1.8 – 2.0,

no degradation, no contamination

PCR Products* ≥ 400 ng ≥ 200 ng ≥ 10 μL ≥ 20 ng/μL OD260/280 = 1.8 – 2.0,

no degradation, no contamination

PCR Products* ≥ 200 ng ≥ 100 ng ≥ 10 μL ≥ 20 ng/μL OD260/280 = 1.8 – 2.0,

no degradation, no contamination

*One PCR product for one library
**Multiple PCR products for one library (at least 2 different PCR products)

5. Epigenetics Sequencing

Library Type Sample Type Amount (Qubit®) Volume Concentration Purity
(NanoDropTM/ agarose gel)
Strongly recommended Required
Whole Genome Bisulfite Sequencing Genomic DNA

(genome size ≤ 1.5 G)

≥ 6 μg ≥ 3 μg ≥ 20 μL ≥ 50 ng/μL OD260/280 = 1.8 – 2.0,

no degradation,

no contamination

Genomic DNA

(1.5G < genome size ≤ 3.5 G)

≥ 12 μg ≥ 6 μg ≥ 20 μL ≥ 50 ng/μL
ChIP-Seq ChIP-Seq DNA ≥ 100 ng ≥ 50 ng ≥ 10 μL ≥ 50 ng/μL Main peak of 100 bp – 500 bp

6. Transcriptome Sequencing

Library Type Sample Type Amount (Qubit®) Volume Concentration RNA Integrity Number
(Agilent 2100)
Purity
(NanoDropTM
Strongly recommended Required
Eukaryotic RNA-Seq Total RNA (Animal) ≥ 2.6 μg ≥1.3 μg ≥ 20 μL ≥ 50 ng/μL ≥ 6.8, smooth base line OD260/280 = 1.8 – 2.2, OD260/230 ≥ 2.0,

no degradation,

no contamination

Total RNA (Plant and Fungus ) ≥ 2.6 μg ≥ 1.3 μg ≥ 20 μL ≥ 50 ng/μL ≥ 6.3, smooth base line
Prokaryotic RNA-Seq Total RNA ≥ 6 μg ≥ 3 μg ≥ 20 μL ≥ 50 ng/μL ≥ 6.0, smooth base line

7. Small RNA Sequencing

Library Type Sample Type Amount (Qubit®) Volume Concentration RNA Integrity Number
(Agilent 2100)
Purity
(NanoDropTM
Strongly recommended Required
Eukaryotic small RNA Sequencing Total RNA (Animal) ≥ 6 μg ≥ 3 μg ≥ 20 μL ≥ 50 ng/μL ≥ 8, smooth base line OD260/280 = 1.8 – 2.2, OD260/230 ≥ 2.0,

no degradation,

no contamination

Total RNA (Plant and Fungus ) ≥ 6 μg ≥ 3 μg ≥ 20 μL ≥ 50 ng/μL ≥ 7.5, smooth base line

8. Long non-coding Sequencing

Library Type Sample Type Amount (Qubit®) Volume Concentration RNA Integrity Number
(Agilent 2100)
Purity
(NanoDropTM
Strongly recommender Required
Eukaryotic Long non-coding RNA Sequencing Total RNA (Animal) ≥ 5 μg ≥ 2.5 μg ≥ 20 μL ≥ 50 ng/μL ≥ 6.8, smooth base line OD260/280 = 1.8 – 2.2, OD260/230 ≥ 2.0,

no degradation,

no contamination

Total RNA (Plant and Fungus ) ≥ 5 μg ≥ 2.5 μg ≥ 20 μL ≥ 50 ng/μL ≥ 6.3, smooth base line

9. Pre-prepared library

(1) Library volume requirement:

Data amount Volume requirement*
< 30 G ≥ 10 μL
≥ 30 G ≥ 20 μL

*High concentration samples should be diluted before delivery

(2) Library concentration: library concentration quantified by Qubit® 2.0 (Life Technologies): ≥ 0.5 ng/uL

(3) Insert size: dilute to 1 ng/µL before checking the insert size by Agilent 2100 Bioanalyzer.

  1. Insert size: insert + adapters (120 bp) ± 50 bp (Does not apply to small RNA library)
  2. Main peak present, no multiple peaks, no adapter contamination and no primer dimers.

(4) Library concentration quantified by Q-PCR:

Platform Concentration requirement
HiSeq 2500 2 nM – 30 nM
MiSeq 4 nM – 30 nM
HiSeq X 3 nM – 30 nM

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PRE-QUALITY CONTROL (QC) INSTRUCTIONS

Customers must provide the results of analysis of sample quality obtained using one of the following methods: Qubit®, NanoDropTM, agarose gel electrophoresis, or Agilent 2100. It is recommended samples be analyzed by Qubit/PicoGreen/gel electrophoresis (with quantity indicator), so that the results will correspond more closely to Novogene QC results. NanoDropTM quantification is NOT recommended. If NanoDropTM is utilized for pre-QC quantification, Novogene strongly recommends that you send more DNA/RNA for processing than the amounts given above.

For gel electrophoresis, the following conditions are recommended:

DNA: 1.0% agarose gel; 1.0% TAE solution; 100V for 40 min
RNA: 1.0% agarose gel; 0.5× TBE solution; 180V for 16 min

Note:
Different electrophoresis conditions may generate a different, and potentially misleading, QC report on your samples. Therefore, it is highly recommended that you adhere to the conditions recommended above for the initial check, and that you provide Novogene with a picture of the gel.

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DEMONSTRATIONS OF QUALIFIED DNA/RNA SAMPLES

1. Demonstration of Markers Used

Novogene utilizes the following molecular size markers for sample quality control testing (Fig. 1).

Demonstrations of Markers
Fig. 1. (A) Trans2K™Plus DNA Marker, (B) λ/HindIII DNA Marker, bp.

2. Demonstrations of DNA sample quality

a) Main types of sample quality
A qualified DNA sample is compared with common types of unqualified samples (Fig. 2):
Novogene Sample Quality
Fig. 2. Examples of DNA quality. (A) Trans2K™ Plus DNA Marker, (B) qualified sample, (C) degraded sample, (D) sample contaminated with RNA, (E) sample contaminated with protein. Red boxes denote areas of contamination.

2.2 Samples with degradation

The gel picture illustrates samples with degradation. Severe degradation can impact the quality of the prepared library and subsequent bioinformatics analysis (Fig. 3):
Degraded Sample
Fig. 3. DNA samples with degradation. Panels A, B, and C demonstrate increasing levels of DNA degradation. M-1, Trans2K™ Plus DNA Marker.

2.3 Samples with RNA contamination

RNA contamination of DNA samples (Fig. 4) can impede the library construction process. It is strongly recommended to digest your DNA samples with RNase before shipping.RNA contaminated samples
Fig. 4. DNA samples contaminated with RNA. Panels A – D demonstrate increasing levels of RNA degradation. Red boxes denote areas of contamination. M-1, Trans2K™ Plus DNA Marker.

2.4 Samples with protein contamination

DNA samples can be contaminated by protein, as illustrated in Fig. 5. It is recommended that you purify protein-contaminated DNA by affinity column. Please note that column purification will lead to some loss of DNA.
Protein contaminated samples
Fig. 5. DNA samples contaminated with protein. Panels A – C demonstrate increasing levels of protein contamination. Red boxes denote areas of contamination. M-1, Trans2K™ Plus DNA Marker.

3. Demonstrations of RNA sample quality

3.1 Main types of sample quality

A qualified RNA sample is compared with common types of unqualified samples (Fig. 6):
Main types of samples
Fig. 6. Examples of RNA quality. (A) qualified sample, (B) samples with protein contamination, (C) samples with degradation, (D) samples with genomic DNA contamination. Red boxes denote areas of contamination. M, Trans2KTM Plus DNA Marker.

3.2 Samples with protein contamination

Protein Contaminated Sample
Fig. 7. RNA samples with protein contamination. Panels A – D demonstrate increasing levels of protein contamination. Red boxes denote areas of contamination. M, Trans2KTM Plus DNA Marker.

3.3 Agarose gel and Agilent 2100 analysis of RNA samples

Agarose Gel Fig 8
Fig. 8. An example of gel electrophoresis (left), and Agilent 2100 (right), results for an acceptable total RNA sample.
Agarose Gel Fig 9
Fig. 9. An example of gel electrophoresis (left), and Agilent 2100 (right), results for a degraded total RNA sample.
Agarose Gel Fig 11
Fig. 10. An example of gel electrophoresis (left), and Agilent 2100 (right), results for an RNA sample with contamination.
Agarose Gel Fig 11
Fig. 11. An example of gel electrophoresis (left), and Agilent 2100 (right), results for a viscous total RNA sample.

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SAMPLE LABELING RECOMMENDATIONS

  1. It is important to prevent the sample labels from being dissolved by solvents and from falling off the tubes. We strongly recommend you use a waterproof marker pen to write directly on the tube wall or lid. You can also write the sample information on a paper/plastic label, stick the label onto the tube wall, and then secure the label to the tube by wrapping with clear, adhesive tape (e.g. Scotch tape) completely around the tube.
  2. Please fill out and attach the Sample Information Form provided by Novogene in the email before shipping the samples. Please make sure that the sample information on the Sample Information Form matches the labels on the tubes.

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SAMPLE PACKING RECOMMENDATIONS

  1. For DNA and RNA samples, Novogene recommends 1.5 ml or 2 ml screw-cap DNase- and RNase-free microcentrifuge tubes. Please use Parafilm to seal each tube before packaging. Novogene does not recommend shipping samples dissolved in organic solvents (such as absolute ethanol or isopropanol) because the solvents may cause leakage of the samples, which can result in cross-contamination between samples. If it is unavoidable to ship samples in organic solvents, please use screw-cap tubes and seal the opening of the tube with at least 10 layers of Parafilm.
  2. In order to avoid crushing during shipping, Novogene highly recommends placing the sample tubes in a container such as a 50-ml tube or a box with interior racks/holders. Cotton and absorbent papers can be used to prevent tubes from moving around inside the container.
  3. RNA samples should be kept in dry ice during shipment. Genomic DNA samples should be kept in blue ice during shipment. Saliva samples should be shipped at room temperature.
  4. In order to stick with our high quality control standards, 96-well plates and PCR stripe tubes are NOT acceptable containers for your sample shipping. The only container we allow for sample shipping is 1.5 ml or 2 ml tube. (See picture below).

Fig12-sample-packing
Fig. 12. Recommended and prohibited tubes for sending samples

COMPLETING THE SAMPLE SUBMISSION FORM

A Sample Information Form must be submitted for each sequencing service project. All information on the forms should be filled out carefully. Please submit the completed ELECTRONIC COPY via email to our local sales representative and enclose a HARD COPY in the shipment. In both copies, please make sure you mark the samples summary (Sample types and number) at the top of the Form (Fig. 13)
Sample Form
Fig. 13. Sample summary (top) and Sample Information Form

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SHIPPING SAMPLES TO NOVOGENE

Disclaimer: The information below only constitutes a recommendation for shipping samples classified as “non-regulated materials” to our facility. At the time this document was prepared, gDNA/total RNA was not defined as a diagnostic specimen in the International Air Transport Association (IATA) packing instructions, and therefore no special packaging requirements are listed. Due to continuing changes in regulations, customers should always check with their safety office and/or shipping department to ensure regulatory compliance.

  1. Ensure that all samples conform to our quality standards and that they are prepared and packaged according to the guidelines given above.
  2. Please make sure to notify a Novogene representative and to send the required documents before shipping your samples.
  3. Depending on your location, you will ship your samples either to our US or Hong Kong sample receiving sites.

Shipping to the US lab
We recommend all US and Canadian customers to ship samples to our US lab at the address below:

Novogene Corporation Inc.
Julie Huang
2921 Stockton Blvd. Suite 1810
Sacramento CA 95817
Tel: 916-701-5130

  1. Select a reliable courier. Novogene recommends FedEx (fedex.com) and UPS (ups.com). For FedEx, we recommend selecting Priority Overnight (arriving next day by 10:30 am) or Standard Overnight (arriving next day by 3:00 pm). For UPS, we recommend selecting Next Day Air (arriving next day by 10:30 am) or Next Day Air Saver (arriving next day by 3 pm).
  2. We recommend sending your samples Monday through Wednesday to avoid possible weekend arrival.
  3. Sample transportation options:
  4. DNA Lyophilize the DNA for shipping at ambient temperature
    Pack with ice packs/blue ice (2-8 °C)
    Use the cold-chain transportation system (2-8 °C) of the courier
    DNA Stable (Liquid format, Biomatrica)
    Pack in dry ice (-60 °C – -80 °C)
    RNA Lyophilize the RNA for shipping at 2-8 °C or ambient temperature
    Suspend RNA in 75% ethanol and ship on dry ice
    RNAstable (Biomatrica)
    Pack in dry ice (-60 °C – -80 °C)
    Note:

    a. It is highly recommended that RNA samples be shipped in dry ice packaging. Other packaging/transportation methods may add impurities or cause slight degradation of the RNA.

    b. The quantity of dry ice and ice bags needed varies with the season (i.e., room temperature), transit time, and the thickness of Styrofoam box and receptacle. Please contact your local courier office for estimated transit time. Normally, dry ice is consumed (sublimates) at a rate of 5 kg (11 pounds) per day.

  5. Package the samples with (1) a completed and detailed Sample Information Form; and (2) include any QC data for the samples if available (Qubit/Nanodrop/agarose gel electrophoresis/Agilent 2100). Pack the DNA and RNA samples according to the above options, and send the package to the address below:

    UC Davis sample receiving address.
  6. Novogene Corporation Inc.
    Julie Huang
    2921 Stockton Blvd. Suite 1810
    Sacramento CA 95817
    Tel: 916-701-5130

  7. Email the Sample Information Form and Purchase Order (PO) to the Novogene sales representative/project manager assigned to your project (indicated in the official quotation). Use the Sample Tracking Quote# xxx as the subject line in the email, and include the tracking information (courier name and tracking number) in the email to help ensure that the samples arrive safely and without any delay.
  8. After arriving at the Novogene site, samples will be stored in a -80 °C freezer. The Project Manager will be responsible for providing timely feedback to you on the progress of your project.

Shipping to Hong Kong

  1. Select a reliable courier and choose the priority option for international shipments. Novogene recommends FedEx (fedex.com), UPS (ups.com), DHL (dhl.com), TNT (tnt.com), and USPS (usps.com). Whichever courier you choose, please make sure that the carrier can facilitate the importation of DNA or RNA samples, and dry ice packing (if applicable), into Hong Kong.
  2. Sample transportation options:
  3. DNA Lyophilize the DNA for shipping at ambient temperature
    Pack with ice packs/blue ice (2-8 °C)
    Use the cold-chain transportation system (2-8 °C) of the courier
    DNA Stable (Liquid format, Biomatrica)
    Pack in dry ice (-60 °C – -80 °C)
    RNA Lyophilize the RNA for shipping at 2-8 °C or ambient temperature
    Suspend RNA in 75% ethanol and ship on dry ice
    RNAstable (Biomatrica)
    Pack in dry ice (-60 °C – -80 °C)
    Note:

    a. It is highly recommended that RNA samples be shipped in dry ice packaging. Other packaging/transportation methods may add impurities or cause slight degradation of the RNA.

    b. The quantity of dry ice and ice bags needed varies with the season (i.e., room temperature), transit time, and the thickness of Styrofoam box and receptacle. Please contact your local courier office for estimated transit time. Normally, dry ice is consumed (sublimates) at a rate of 5 kg (11 pounds) per day.

  4. Contact your local international courier and complete an INVOICE (commercial invoice, customs invoice, or pro-forma invoice) as required for customs, and include it with the shipment. Please complete the INVOICE as below:

    a. RNA or DNA Samples for Research Use Only
    b. Non-Dangerous, Non-Infectious
    c. No Commercial Value, Value for Customs Only
    d. Declare the value of the goods for customs [i.e. $1.00 (USD) or €1.00 (EUR)]
    e. Number of samples and volumes [the # of samples, and the estimated volume]
    f. Type of container

Sample Invoice
Fig. 14. Courier INVOICE Example

  1. Package the samples with (1) a completed and detailed Sample Information Form; and (2) include any QC data for the samples if available (Qubit/Nanodrop/agarose gel electrophoresis/Agilent 2100). Pack the DNA and RNA samples according to the above options, and send the package to the address below. (Note: there is no zip code/postal code system in Hong Kong)

    Hong Kong sample receiving address:
  2. Novogene Bioinformatics Technology Co., Ltd
    NO.53, KAM POK ROAD, Yuen Long, N.T, Hong Kong
    ATTN: GARY CHAN
    Tel: +852 60385860

  3. Email the Sample Information Form and Purchase Order (PO) to the Novogene sales representative/project manager assigned to your project (indicated in the official quotation). Use the Sample Tracking Quote# xxx as the subject line in the email, and include the tracking information (courier name and tracking number) in the body of the email to help ensure that the samples arrive safely and without any delay.
  4. After arriving at the Novogene site, samples will be stored in a -80 °C freezer. The Project Manager will be responsible for providing timely feedback to you on the progress of your project.

Qubit is a trademark of Life Technologies and Thermo Fisher Scientific.
NanoDrop is a trademark of NanoDrop Technologies LLC.
Agilent 2100 Bioanalyzer is a trademark of Agilent Technologies.
Trans2K Plus is a trademark of TransGen Biotech.

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