Set protein panels

Protein panels

Choose one appropriate panel depending on the organism. The protein panel is required in PID mapping.

Species	Protein panel	MD5	Cocktail information
mouse	ProteinPanel_128_mouse_V2.list	8745033762db89d5a4096232e54e6521	TotalSeq-A™ Mouse Universal Cocktail, V1.0 (Cat. No. 199901)
human	ProteinPanel_163_human_V2.list	64a20baa464ba38aa1f7f93286b18bed	TotalSeq-A™ Human Universal Cocktail, V1.0 (Cat. No. 399907)

*Know more details according to Cocktail information.

wget

#mouse
wget -c https://demo.stomicsdb.tech/STOmics_Reference_Released/Protein_Panel/ProteinPanel_128_mouse_V2.list

#human
wget -c https://demo.stomicsdb.tech/STOmics_Reference_Released/Protein_Panel/ProteinPanel_163_human_V2.list

curl

The panel specifies antibodies used in the Stereo-seq proteo-transcriptome co-detection experiment. Each column is separated by Tab. The table displays column description in the panel:

Column name	Decription
PIDIndex	Required. Protein index. Only accepts integer numbers and ensures each is unique.
PIDSequence	Required. Protein reference sequence in 15bp.
PIDName	Required. Only accepts letters [a-zA-Z], digits [0-9], and 4 symbols ["(", ")", "-", "_"].
GeneName	Required. Coding gene(s) of the corresponding protein. Multiple coding genes are separated by "/". If you don't know, please fill in None.
GeneID	Required. Coding gene(s) Ensembl ID. Multiple IDs are separated by "/". If you don't know, please fill in None.

Reference libraries

A CSV of --ref-libraries can be built to combine the protein panel and Transcriptome STAR reference.

Reference,Type
/saw/datasets/reference/transcriptome,STAR
/saw/datasets/reference/ProteinPanel.list,ProteinMap

This CSV of --ref-libraries is required in SAW count analysis for Stereo-CITE solution.