Closed ESapenaVentura closed 2 years ago
Started wrangling but it's a difficult dataset - Contains assembloids
I will contact @ami-day when capacity allows
Shall we discuss this dataset tomorrow @ESapenaVentura ?
Hi @ESapenaVentura I have completed the unfilled metadata and added ontologies. Also, we should discuss the experimental design. I have highlighted in yellow some differences to how I would have modelled it, in particular to:
cell_line.biomaterial_core.biomaterial_id (I think I wouldn't use this tab)
organoid.biomaterial_core.biomaterial_id
aggregate_generation_protocol.protocol_core.protocol_id
differentiation_protocol.protocol_core.protocol_id
Maybe we could go through it sometime on Monday.
@Wkt8 to do the secondary review
Hi Ami. I had a look at the existing spreadsheet and noted down where I think things should be modelled differently / were not filled in. Overall I agree with the assembloids being modelled as organoids generated from the existing organoids and purified cells, but have noted down some changes below in the respective tabs. Let me know if you have any questions!
Donor Organism Tab:
Collection protocol:
Specimen_from_organism
Cell_line
Organoid
Cell suspension
Analysis protocol
Sequence_file
Thanks @Wkt8 , re-reading the Methods, I agree with all your suggested changes and have made them, except for this one:
"The endometrial gland-like organoids have a 'specimen_from_organism' as the input. I would have modelled it as the cell_line as the input."
In the Endometrial gland-like organoid culture Methods section, it says "Freshly isolated endometrial gland fragments were resuspended...". This suggest to me that the input material is primary tissue specimen. Then, the EnSCs and the gland-like organoids are then used as input for the Establishment of assembloid cultures
Hope that sounds ok to you!
Will download the fastq files now.
Downloading the fastq files. Submission: https://contribute.data.humancellatlas.org/submissions/detail?uuid=e36ea62d-cecf-48fa-a1a2-6e202e2071e3&project=91af6e2f-65f2-44ec-98e0-ba4e98db22c8
Checked that the number of donors look right, health status, tissues, and number of data files/matrices. All of that looks alright
However, the data curator is missing. Moving to needs update
Added the curator (me): https://contribute.data.humancellatlas.org/submissions/detail?uuid=e36ea62d-cecf-48fa-a1a2-6e202e2071e3&project=91af6e2f-65f2-44ec-98e0-ba4e98db22c8 but the status stayed as "exported" ?
Submitted update.
exported.
looks as expected in the hca data portal.
Project short name: dcp4780289864815075
Primary Wrangler: @ESapenaVentura / @ami-day
Secondary Wrangler:
@ami-day / @ESapenaVentura
Associated files
Latest google sheet: https://docs.google.com/spreadsheets/d/1MKzczXQV94nZHhSCiLWElAMhpeCe7Cjk2bZXZg_4g5Y/edit#gid=390429689
Published study links
Paper: https://elifesciences.org/articles/69603
Accessioned data: GSE168405
Key Events