Update suspension_type

[brianraymor]

Design

Additions

For Assay	MUST Use
mCT-seq [EFO:0030060]	"cell" or "nucleus"
MERFISH [EFO:0008992]	"na"
methylation profiling by high throughput sequencing [EFO:0002761] and its descendants	"nucleus"
ScaleBio single cell RNA sequencing [EFO:0022490]	"cell" or "nucleus"
sci-RNA-seq3 [EFO:0030028]	"cell" or "nucleus"

Deletions

For Assay	MUST Use
CITE-seq [EFO:0009294] and its descendants	"cell"
smFISH [EFO:0009918] and its descendants	"na"
snmC-seq [EFO:0008939]	"nucleus"
snmC-seq2 [EFO:0030027]	"nucleus"
spatial proteomics [EFO:0700000] and its descendants	"na"

Notes

Additional assays can be added to suspension_type.

Types from @jychien:

1. ~mCT-seq: “cell” or “nucleus”~
2. ~ScaleBio: “cell” or “nucleus”~
3. ~methylation profiling by high throughput sequencing: The current children are both “nucleus”. Methylation is typically done on nucleus, but I am guessing we’ll need to revisit if there are new decedents in the future.~

Note from @jahilton: With the updated submission policy, our only smFISH Datasets (which are private) will be removed, and no more will be accepted. So the smFISH and its descendants row can be simplified to MERFISH EFO:0008992

That assay list review...

• ~remove "CITE-seq and its descendants"~
• ~replace "smFISH and its descendants" with "MERFISH EFO:0008992"~
• ~remove "snmC-seq"~
• ~replace snmC-seq2 with "methylation profiling by high throughput sequencing [EFO:0002761] and its descendants"~
  • ~we need to cover snm3C-seq as all our existing "methylation profiling..." datasets will be revised to that~
• ~remove spatial proteomics and its descendants~

The list of assays must also be reviewed to eliminate cases that are not supported such as cite-seq.

[brianraymor]

Show the math. Current set of assays:

assay	addressed by
"10x 3' transcription profiling",	10x transcription profiling [EFO:0030080] and its descendants
"10x 3' v1",	10x transcription profiling [EFO:0030080] and its descendants
"10x 3' v2",	10x transcription profiling [EFO:0030080] and its descendants
"10x 3' v3",	10x transcription profiling [EFO:0030080] and its descendants
"10x 5' transcription profiling",	10x transcription profiling [EFO:0030080] and its descendants
"10x 5' v1",	10x transcription profiling [EFO:0030080] and its descendants
"10x 5' v2",	10x transcription profiling [EFO:0030080] and its descendants
'10x multiome',	ATAC-seq [EFO:0007045] and its descendants
'10x scATAC-seq',	ATAC-seq [EFO:0007045] and its descendants
'BD Rhapsody Targeted mRNA',	BD Rhapsody Targeted mRNA [EFO:0700004]
'BD Rhapsody Whole Transcriptome Analysis',	BD Rhapsody Whole Transcriptome Analysis [EFO:0700003]
'CEL-seq2',	CEL-seq2 [EFO:0010010]
'DroNc-seq',	DroNc-seq [EFO:0008720]
'Drop-seq',	Drop-seq [EFO:0008722]
'GEXSCOPE technology',	GEXSCOPE technology [EFO:0700011]
'inDrop',	inDrop [EFO:0008780]
'MARS-seq',	MARS-seq [EFO:0008796]
'mCT-seq',	mCT-seq [EFO:0030060]
'MERFISH',	MERFISH [EFO:0008992]
'microwell-seq',	microwell-seq [EFO:0030002]
'Patch-seq',	Patch-seq [EFO:0008853]
'ScaleBio single cell RNA sequencing',	ScaleBio single cell RNA sequencing [EFO:0022490]
'scATAC-seq',	ATAC-seq [EFO:0007045] and its descendants
'sci-Plex',	sci-Plex [EFO:0030026]
'sci-RNA-seq',	sci-RNA-seq [EFO:0010550]
'sci-RNA-seq3',
'Seq-Well',	Seq-Well [EFO:0008919] and its descendants
'Seq-Well S3',	Seq-Well [EFO:0008919] and its descendants
'Slide-seqV2',	spatial transcriptomics [EFO:0008994] and its descendants
'Smart-seq',	Smart-like [EFO:0010184] and its descendants
'Smart-seq v4',	Smart-like [EFO:0010184] and its descendants
'Smart-seq2',	Smart-like [EFO:0010184] and its descendants
'snm3C-seq',	methylation profiling by high throughput sequencing [EFO:0002761] and its descendants
'snmC-Seq2',	methylation profiling by high throughput sequencing [EFO:0002761] and its descendants
'SPLiT-seq',	SPLiT-seq [EFO:0009919]
'STRT-seq',	STRT-seq [EFO:0008953]
'TruDrop',	TruDrop [EFO:0700010]
'Visium Spatial Gene Expression'	spatial transcriptomics [EFO:0008994] and its descendants