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StanfordBioinformatics / pulsar_lims

A LIMS for ENCODE submitting labs.
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ENCODE submission: 9 fetal heart samples for Bei #968

Closed twang15 closed 1 year ago

twang15 commented 1 year ago

Hi Bei,

To initiate the encode data submission for the 9 fetal heart samples, I have shared with you two links:

  1. https://docs.google.com/spreadsheets/d/1bNWmvYvaTIbAxehb36gs2c9r8rYRwMDv/edit#gid=1373738345 This is the submission sheet that we are going to work on together. The order is from left to right, donors, biosamples, experiments, libraries, replicates and files. Each of the tabs must be filled out and then submitted before the preparation of the next one can be initiated. Now we are on the first one: donors.

  2. https://docs.google.com/spreadsheets/d/185zIjoScm7JuJeljuzgO5tTO1e5ilpjeJQ4PQ_hV5Uw/edit#gid=0 This is an example submission that we finished before. If you are not sure what value goes to each field, it is a good reference.

Please fill out 1st sheet to your best knowledge and let me know if you have any questions.

Best, Tao

twang15 commented 1 year ago

Hi Emma,

I’ve resolved your comments. Could you please fill in column I for “age” in the unit of day?

Best, Tao

twang15 commented 1 year ago

Hi Emma,

Here is the link to the document: /documents/c4b8952c-d9f1-42e7-8ea5-54659d14f46b/. I am not sure whether it has to be updated. It depends on what was done in the biosample preparation.

https://www.encodeproject.org/documents/c4b8952c-d9f1-42e7-8ea5-54659d14f46b/@@download/attachment/ENCODE4_Snyder_HumanTissuePreservation_Flash_v1.pdf

@Shin and Yiing, please let us know the right source so that we can proceed.

Best, Tao

twang15 commented 1 year ago

Hi Jennifer,

Could you help register the vendor for “Birth Defects Research Laboratory “ in ENCODE and let me know the ENCODE ID?

Thanks, Tao

twang15 commented 1 year ago

waiting for Ian and then proceed from here: https://docs.google.com/spreadsheets/d/185zIjoScm7JuJeljuzgO5tTO1e5ilpjeJQ4PQ_hV5Uw/edit#gid=0

twang15 commented 1 year ago

Hi Bei,

The 9 heart sample submission depends on your inputs. Please fill the “files” tab and let me know once it is ready. https://docs.google.com/spreadsheets/d/1bNWmvYvaTIbAxehb36gs2c9r8rYRwMDv/edit#gid=1861576654

Best, Tao

twang15 commented 1 year ago

Done