Create metadata schema for a new assay: SLIDEseq

[cebriggs7135]

Here's a link to the spreadsheet for SLIDEseq metadata: https://docs.google.com/spreadsheets/d/1KDBigt6Kqi7VRFb_uc3zkc17tedi4gz_oS0Y2T0fi08/edit?usp=sharing It's much the same as RNAseq except for a new puck_id column.

[mccalluc]

@cebriggs7135 : Do you mean bulkrnaseq? Or sc? Or something else? Is there a portal-docs for this yet? what about directory schema?

[cebriggs7135]

SLIDEseq is most like single cell RNA seq because the RNA transcripts are captured on beads associated with spatial coordinates on a slide (rather than bead per cell).

Is completion of these documents below a blocker to generating the assay metadata schema?

The directory structure doc here (1) & the assay document (2) are undergoing some updates by the Broad team per a sprint we (Alex & I) had with them on Wednesday:

(1) https://docs.google.com/document/d/1k3Q48rkL_ueA4_8NTaTLtBfNCG0fa8LwsXqP9O5gILo/edit?usp=sharing (2) https://docs.google.com/document/d/1og-cHmOlfX0YIIfBqRnWnSe3w9_44T0KilN3GAxPnW8/edit?usp=sharing

[mccalluc]

@cebriggs7135: Confirm that the sc_* fields should be dropped, along with library_id?

scrnaseq:                               slideseq:

...
acquisition_instrument_vendor       acquisition_instrument_vendor
acquisition_instrument_model        acquisition_instrument_model
sc_isolation_protocols_io_doi     <
sc_isolation_entity       <
sc_isolation_tissue_dissociati    <
sc_isolation_enrichment       <
sc_isolation_quality_metric   <
sc_isolation_cell_number      <
rnaseq_assay_input        <
rnaseq_assay_method         rnaseq_assay_method
library_construction_protocols      library_construction_protocols
library_layout              library_layout
library_adapter_sequence        library_adapter_sequence
library_id            | puck_id
is_technical_replicate          is_technical_replicate
...

[cebriggs7135]

@mccalluc That is not the correct template. Other fields are also absent for SLIDEseq. The template is here: https://docs.google.com/spreadsheets/d/1KDBigt6Kqi7VRFb_uc3zkc17tedi4gz_oS0Y2T0fi08/edit#gid=1112128153

[mccalluc]

@cebriggs7135 -- Could you make this comment on the active PR instead? Since that's the same URL you gave above, and can say more precisely what fields are missing?