idazucchi
commented
2 years ago Hi Ami! I'm done with the secondary review. Most of the dataset is all right, but I have a few comments/suggestions
Donor
- I would put mouse embryo stage in
developmental stagefor the mouse donor - The gestational age for the mouse is missing
Collection protocol
- the mouse collection protocol is missing from the paper, but it could be the same as Delile et al., 2019. Both papers are from the same lab
Specimen
- CS17 was stored for 24h before processing, you could record that
- I would remove the INSDC experiment accession
Cell suspension
- the
descriptionhas a typo, all the information are repeated - the INDSC sample accessions are missing
- you could fill in the cell viability field
- cell estimate counts are available in the supplementary table 1, available through a link in the supplementary materials
- the dissociation protocol doesn’t match the ID of the existing protocols
Library preparation
- you could add the library preparation kit name
Sequence file
- you could fill in the read length
Analysis protocol
- you could add the computational method
Analysis file
- it would be more informative to decompress the tar archives and list each file individually so that the file descriptors can be more specific
- the checksum is filled in with the cell suspension ID, but the cell suspension ID for the second matrix should be
SRX10579581||SRX10579582
ami-day
Ingest https://contribute.data.humancellatlas.org/projects/detail?uuid=6621c827-b57a-4268-bc80-df4049140193&tab=project
Publication https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8353162/
Google Sheet https://docs.google.com/spreadsheets/d/1U2a-vmHvNYGyzgWQe0_IdOuzZanI65w31Mc3eu_lFxQ/edit#gid=670206729
Primary wrangler Ami
Secondary wrangler Ida