The cell lines and data browser gives an overview of HipSci cell lines and assay data that are publicly available. It also provides links to publicly available HipSci data in the EBI data archives.
Data are submitted to various open access data archives, depending on the data type:
The cell lines and data browser will guide you to the correct archive and download link for your chosen data. Start at the files table and enter a search term, or use the table filters to discover available data.
Managed-access genetic and genomic data
This data is accessible upon the completion of a Data Access Agreement via the Wellcome Trust Sanger Institute’s Electronic Data Access Mechanism.
The eDAM website
The eDAM page on the Sanger Institute website is the home of applications for HipSci’s managed access data. This is where you apply for access to a HipSci cohort in the EGA archive. The data page of the HipSci website has a button labelled ‘access managed data’, which will take you to the relevant eDAM page.
Step 1: Register your email address
You must be a registered user of the eDAM system before you can apply for HipSci data access. Click on the button “Register now” on the eDAM front page, and then fill out your email address and create a password. You will receive an immediate automated email with a link to complete your registration.
Step 2: Complete your registration as a user
Follow the link in the automatic email from step 1 to authenticate email, and then log in to eDAM. On the “Welcome to eDAM” page, click the button to “continue”. Next, click the button to “Complete Registration”. You must complete all three pages of the registration form, and then click the button “submit form”
You are now a registered user in the eDAM system, but you have not yet applied for data access. You must proceed to step 3 to start applying to HipSci data sets.
Step 3: Start an application
Start from the eDAM page on the Sanger institute website. Log in to the system using your user name and password that you generated in step 1.
On the “Welcome to eDAM” page, click the button to “continue”. On the project page, click on the button to “start a new application”.
The next page presents a list of agreement types. You should select “HIPSCI”.
There are three pages with terms of agreement. On pages 1 and 2, read the terms of agreement and then press “continue”.
On page 3 of 3 you will need to select the cohort for which you seek data. You will apply for access to all the data generated for any cell line belonging to the selected cohort.
You can select more than one cohort if you require access to more than one. It is wise to only select the cohorts you need, because you must also provide a summary of the project for which you require the data. The Data review committee can choose not to grant you access if they cannot see a justification for your need of the data.
Once the application page is complete and you agree to the terms, click to submit the form.
Step 4: Your application is processed
Immediately after submitting an application, you will receive an email to confirm your agreement is with your Institutional Representative (IR) for their approval. The data access committee at the Wellcome Trust Sanger Institute will then review your application.
Later, once access is granted, you will receive an email stating:
“The application for your chosen dataset (request-ID xxxx) has been approved and appropriate permissions generated for you at the EGA. If you are new to the EGA, login and password details will be sent under separate cover directly from the EGA. If you do not receive these in the first instance please check your junk email. If you are an existing EGA user please log into your account as normal, to see the additional datasets. If you have any technical difficulties accessing your account or the data please contact the EGA directly on email@example.com”
Step 5: Access the data from EGA
The European Genome-phenome Archive (EGA) is a service for managed access distribution of individually unique data from biomedical research projects.
If your application was successful, you will now have login details for the EGA. You can login, locate the HipSci data and begin to download the data for the cohort you selected. You will have access to any data that has been deposited already as well as any data we deposit for the cohort in the future.