Onboarding Instructions for PhIP-Seq: Studies where the client is able to aliquot samples into CDI-provided plates (Intake 1).
Step 1: Prepare and submit a PO matching your Quote ID.

Please do not prepare or ship samples until you have created an official purchase order (PO) from your company or institution matching the chosen quote. Keep track of your Quote ID as you will need it for filling out forms and can use it to get updates on your project status.

To proceed with official onboarding, please submit a PO for your chosen quote in PDF format – not just the PO# – to:

Nina Cummings

[email protected]

Please be sure to mention your Quote ID or re-attach your quote PDF to your order email.

While waiting for your PO – you can learn more about our onboarding process and begin preparing documents and metadata for onboarding on this page. All information you will need for your onboarding questionnaire is provided below. Please prepare it in advance to speed up your future onboarding survey.

If you have questions or need help – please email:

[email protected]

Step 2: Understand the onboarding overview.

You have chosen to aliquot your own PhIP-Seq samples into CDI-provided plates for processing and analysis. This will help your study proceed more quickly. Thank you!

Please follow the instructions below for filling out your documents carefully.  Our process is highly automated and our pipelines depend on these manifests being completed as indicated.

We will need a completed source manifest, completed shipping declaration forms, and completed shipping contact information for each quoted project. Each will be addressed more further down on this page. You can fill it out now, but will be submitting it later.  You can also download everything right here:

Source Manifest Instructions

Source Manifest Template

Aliquoting, Declaration, and Shipping Instructions

Shipping Declaration Forms – Human products (if applicable)

Shipping Declaration Forms – Human CSF products (if applicable)

Shipping Declaration Forms – Mouse products (if applicable)

This information will all be requested directly via an onboarding survey once we have received your PO. The purpose of this page is to help you prepare for that onboarding survey.  After you complete the survey, and once we verify that your documents are in order, we will ship you our source sample onboarding kit. This kit will include all the materials and detailed instruction you need to aliquot, package, and ship your samples to our screening lab in Baltimore.

Step 3: Download the Source Manifest and label it with your Quote ID.

Source Manifest Summary

This represents the basic metadata we need to process your samples and track them correctly. You will also need to follow this for aliquoting.

Download a copy of the source manifest here.

Source Manifest Labeling Instructions

It is critical that you completely fill out the source manifest as indicated because our process is highly automated. Your source manifest needs to be uniquely named to serve as an index for all further downstream applications. Your first step is to download it and relabel the final section to match your quote ID.

The file above is labeled: sourceManifest_template.xlsx

You need to relabel it: sourceManifest_YOURQUOTEID.xlsx

Example: If your quoted HuScan study quote is labeled: CNCI230201_SPH12.pdf

You should rename your manifest as: sourceManifest_CNCI230201_SPH12.xlsx

Step 4: Review sample acceptance, shipping, and aliquoting requirements.

Shipping and handling

Please follow these guidelines to ensure your samples arrive safely, securely and without incident.

It is the customers responsibility to be certain of the shipping permits for biological samples to and within the US even if the country of origin does not require an export or import permit. Regulations that govern the transfer of biological materials help to minimize or eliminate possible threats to public health. Sources of information are:



CDI LABS does not accept Category A Infectious Substances (UN2814) such as Ebola or HIV. Please review the following guide for examples of category A infectious substances:


Kits that fail to meet these requirements will not be processed and the source plates will be discarded without exception.

Some countries, couriers and airlines restrict the importation or transportation of some hazardous materials (e.g., dry ice). It is the customers responsibility to determine these restrictions prior to shipment/transport.


Please use the labware we provide you. Other PCR seals may bubble during shipping resulting in contamination and spillage of samples. Sealing tape or seals that require heat are insufficient for transport. Semi-skirted PCR plates crack easily during transport and are not compatible with our automation systems.

Sample Volume

Please aliquot exactly the volume per well indicated per sample type on Table 1. This volume is crucial for automation compatibility. Do not use more than the amount indicated per sample type as this creates a splash hazard and can lead to cross contamination when unsealing the plates.

Sample Aliquoting

Your source manifest indicates what PhIP-Seq library the samples will be screened against. Therefore, you must fill out one source manifest per PhIP-Seq library requested. Please aliquot your samples according to the sampleType and sampleName columns in the source manifest. The source manifest and plates are uniquely named to correspond to your quote and source plate number. These link your samples to their aliquoted location for all downstream processing. Samples must be filled out row wise, starting at well A1  → A12, then proceeding to the next row B1 → B12, and so on down the plate. These coordinates are listed in your source manifest. Source Manifests that do not match the quote or the aliquoted plate layout will not be processed without exception.

Dilution Buffer composition

All dilutions must be made using molecular biology grade 1x PBS ( –Ca and –Mg).

Table 1. Sample types accepted and volumes required

Sample TypeVolume per well (µL)Required concentration
serumNeat20Neat serum/plasma
serumDiluted202 μL serum/plasma + 18 uL dilution buffer
mAB500.1 mg/mL mAb
Step 5: Fill out your Source Manifest.

Your source manifest also indicates what PhIP-Seq library the samples will be screened against. Therefore, please note that you must fill out one source manifest per PhIP-Seq library requested, just as you have received one quote per library.

Now that the file is properly labeled, it is time to fill out the manifest itself. This should be opened in a spreadsheet program like Microsoft Excel or Google Sheets. Please save it as an Excel file (.xlsx).

Please fill out the columns labeled as phipLibrary, sampleName, and sampleType as follows:

phipLibrary is only a single cell (cell A2) that indicates what PhIP-Seq library the samples within the source manifest will be screened against. Type ‘human’ for HuScan. Type ‘mouse’ for MouseScan.

sampleName will link your source plate and well coordinate to your provided sample name. Please type in a string that does not include special characters or spaces and  is between 4 to8 characters. Please leave any unassigned wells blank.

sampleType will inform our liquid handlers how much volume of your sample to carry into the PhIP-Seq assay.  Please type ‘neat’ to indicate you will provide 20 uL of undiluted serum or plasma, ‘diluted’ to indicate 20 uL of serum or plasma diluted 1:10 in PBS (2 uL sample + 18 uL PBS), ‘csf’ to indicate 50 uL of undiluted csf, or ‘mab’ to indicate 50 uL of a 0.1 mg/ml monoclonal solution. It is critical for our liquid handlers that you provide exactly the volumes requested.

Step 6: Download and fill out your Shipping Declaration Forms

These forms relate to the physical samples you are submitting for analysis. They are important for including with your shipment to assure your samples do not get stopped by customs or other regulators. For detailed shipping information please review:

Aliquoting, Declaration, and Shipping Instructions

Please select the form most closely representing your submitted sample type. Modify them as-necessary to adequately describe your samples. You will need to include these documents in your shipment package as well as upload them to the onboarding questionnaire after we receive your PO:

Shipping Declaration Forms – Human products (if applicable)

Shipping Declaration Forms – Human CSF products (if applicable)

Shipping Declaration Forms – Mouse products (if applicable)

Baltimore, MD 21224

[email protected]

Please remember to meticulously follow the instructions provided in your kit. CDI LABS is not responsible for any customs declaration(s) or loss of sample integrity during shipment.

Contact the assay lab with a tracking number at [email protected].

If you have any questions, please contact your sales representative.

Step 7: Know and be ready to enter your contact information.

We will need the information below both for billing, and to know where to send your plates. Items like a phone number are required by some shippers and are essential to quickly resolving shipping challenges.

Contact information (Primary Investigator – for data delivery)




Full Address:

Contact information (Study Contact – Preferred receiving address for aliquot kit to prep your samples for shipment if different from above):




Full Address: