Closed Wkt8 closed 2 years ago
Waiting to get additional metadata from HDBR.
Peng has mentioned that there are additional donors that he would like to add to this project, and he expects it to be in the DCP around August. Am waiting on him to send us additional information on the new donors.
Peng messaged me today saying the ATAC-seq, BCR and TCR data are ready to submit.
Wrangled scRNA, scATAC-seq, VDJ, and organoid data.
Still waiting on some metadata from Peng on the VISIUM donor metadata. Need to email HDBR to get some metadata for scATAC-seq donors.
almost done with archiving Visium data almost done with ATAC-seq data the Visum data will not be in release 12 but the rest of the data will be
We are now archiving this all in Annotare - and they have to be split up into different technologies, which has added a lot more work.
@Wkt8 to make 4 separate Array Express submissions, as technologies need to be separated.
It would be useful if he could move the files from HCA-util to annotare. @Wkt8 to create a ticket in operations
There were some issues with the uploaded fastqs, Wei is looking into this
I have had to split Peng's dataset into four different ArrayExpress submissions:
These have all been submitted to ArrayExpress and will have accessions to send to Peng.
The export to the DCP has not been done yet because Peng is still uncertain about the date for that to go public. The spreadsheet will be in the brokering drive. It probably will not have Visium data added to it yet due to the metadata schema change not being complete which allows imaging (probe and channel) to be optional.
Remaining actions:
Files are available in the hca-util upload area with uuid 4777804d-1b93-4bbf-955f-1c5083e2c504
@idazucchi to sec review
Hello! I'm done with the secondary review. There is so much going on in this dataset! It's mostly good, but I have some comments Let me know if you have any question
MR/S035907/1
is repeatedHDBR1915, HDBR2174, HDBR-N13393
HDBR donors? You could fill in the HDBR accession fieldHDBR1915, HDBR2174, HDBR-N13393
, from the Fetal_lung tab CS23, 8pcw, 8pcw
HDBR1915, HDBR2174, HDBR-N13393
should match their gestational agenormal
HDBR15415
for visium seems to be missing?WSSS_F_LNG8713181specimen, WSSS_F_LNG8713189specimen, WSSS_F_LNG8713191specimen, WSSS_F_LNG8713180specimen, WSSS_F_LNG8713188specimen, WSSS_F_LNG8713190specimen
, they are orphansnormal
WSSS8012016specimen, WSSS8011222specimen
have barker_lab_collection_protocol
?5891STDY9030810specimen
and pool the specimen at the cell suspension level15415-LNG--FO-2_specimen
the donor should be HDBR15415
organoid_lentiviral_induction
you could add the doi 10.1101/2021.06.30.450501
, the differentiation medium and small moleculesMACS_depletion
is not formatted correctlyCD326MACS_optional_4b
is empty5891STDY9030810_CS
should have as input specimens 5891STDY9030806_8specimen||5891STDY9030807_9specimen
scRNA and ATAC-seq CS
SIGAA10, SIGAB10, SIGAC10, SIGAE6, SIGAF6, SIGAG12, SIGAG6, SIGAH10, SIGAH12, SIGAH4
are these sequenced with the novaSeq6000? they are not in the list in tab Fetal_Lung
Have made updates from Ida's secondary review, and am waiting on Peng to give an updated h5ad analysis_files
This is in graph-valid state. Can be exported.
Exporting triggered. Once it has been confirmed that the project has exported, I will fill in the DCP Import Requests form.
@ke4 and @jacobwindsor to investigate it
Triggered exporting again.
@ke4 and @amnonkhen monitored the exported and found that it finished
Exported! Import Request for Production form submitted.
Primary Wrangler: Wei Kheng Teh
Secondary Wrangler: Ida
Associated files: Link to paper: https://www.biorxiv.org/content/10.1101/2022.01.11.474933v1.full Google Drive: https://drive.google.com/drive/folders/19zWssnTCxFEIqj1AqZDRNWFrGrOlIz8m Link to Ingest: https://contribute.data.humancellatlas.org/submissions/detail?uuid=0b53d1ad-bc5f-4030-818b-b12c7ddf5b6c&project=2fe3c60b-ac1a-4c61-9b59-f6556c0fce63
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