MorPhiC Data Contribution Guide

1. Register your study
2. Fill out metadata spreadsheet
   1. Example study and metadata
3. Share the protocols
4. Upload the dataset
5. Feedback on the process

1. Register your study now

The Morphic studies list contains a record of all MorPhiC studies that will generate datasets. The list is being updated by the MorPhiC Data Production Centres (DPC).

When you (as a member of a DPC) have a new study, enter it in the studies list above, providing details like assay type, target genes, and expected timelines.

As soon as a dataset for one of your studies is ready to upload, notify the MorPhiC data team at [email protected] or on the dedicated Slack channel.

A dataset upload area will be created for you, and we will send out login details (to be used in Step 4).

2. Fill out metadata spreadsheet

In addition to uploading the dataset generated from your study, you are required to supply experimental metadata and protocols.

A metadata spreadsheet template is available to download and needs to be populated with metadata about your dataset.

The spreadsheet is designed to capture information at the level of:

• Cell line
• Differentiated cell line
• Expression Alteration strategy
• Library prep
• Sequence files

To understand how the metadata is organised and captured, review the example study and the prefilled metadata spreadsheet below.

i. Example study and metadata organisation

In the diagram below, we have shown an example of the experiment design for a MorPhiC study.

Starting from a single parental cell line, the study features 2 different sets of knockout strategies. From the resulting products, several clones are created and a few are selected, creating 2 branches:

graph LR;
A[KOLF2.2J];
B[kolf2_knock1_a];
C[kolf2_knock1_b];
E[kolf2_knock2_b];
F(Expression alteration strategy 1);
G(Expression alteration strategy 2);
J(Differentiation protocol A);
K(Differentiation protocol B)
H[kolf2_knockout1_cloneA_differentiationA_1day]
L[kolf2_knockout1_cloneB_differentiationB]
M[kolf2_knockout2_cloneB_differentiationB]


A-->F
A-->G

F-->B
F-->C
G-->E

B-->J
C-->K
E-->K

J-->H
K-->L
K-->M

Loading

• A branch with 2 clones selected (kolf2_knock1_a, kolf2_knock1_b) that underwent the expression alteration strategy 1
• A branch with only 1 clone selected (kolf2_knock2_b) that underwent the expression alteration strategy 2

Each of these clones underwent a differentiation protocol, resulting in three end products (kolf2_knockout1_cloneA_differentiationA_1day, etc), referred to the differentiated cell line in the metadata spreadsheet.

The differentiated cell line then undergoes transcriptomics profiling (Library prep to generate Sequence files) and/or phenotyping (e.g. lipidomics).

The metadata for the above study is captured in this example spreadsheet.

This spreadsheet, together with the data files will form a dataset, to be uploaded to your folder.

As this is the initial version of our metadata standard and spreadsheet, we welcome all feedback from DPCs on required metadata and organisation. Please reach out to [email protected] or on the dedicated Slack channel with feedback on how well we capture your studies.

3. Share the protocols

You must complete the Protocols tab in the Morphic studies list.

• When protocols.io DOI is not available, the protocol documents should be uploaded to the individual folder under DPC Protocols in Google Drive. Please see Example_EBI rows in this tab, as well as the Example_EBI folder for reference.
• The PROTOCOL NAME entered in Protocols tab of Morphic studies list must match the name of the associated protocol document submitted to the DPC Protocols.

4. Upload the dataset

To upload your dataset, you will need the morphic-util command-line tool.

You will use the user credentials and an upload area set up from Step 1. Follow the morphic-util Dataset upload instructions to upload:

• A filled out metadata spreadsheet
• Your data files

5. Feedback on the process

As this is the initial version of our Data Contribution Service, we welcome all feedback from DPCs on the process. Please reach out to [email protected] or on the dedicated Slack channel with feedback.