Metadata for P28 data

[salwanbutrus]

Hello,

Thank you for making your code and data available! Would you mind also sharing the metadata for the P28 cells?

Thanks,
Salwan

[gs512]

metadata has been uploaded to the 0_DATA folder

[salwanbutrus]

Thanks for the quick response! The supertype_label for Fishell_P28 data is NaN in integrated_meta_jun28.csv.gz.

[gs512]

If you check https://github.com/gs512/slideseq-engine/blob/main/A_scRNA_prep.ipynb

you can find the following code in the FIG1A cell which gets you the annotation that I'm assuming you're looking for

is that right ?

## FIG 1A

my_ord_v1 = c('SST-Mme', 'SST-Calb2', 'SST-Hpse', 'SST-Etv1','SST-Myh8',
              'SST-Syndig1l', 'SST-Crh','SST-Nmbr', 'CHODL')
P28_sst@meta.data$sherry_clusters = dplyr::recode(P28_sst@meta.data$seurat_clusters,
'4' ='SST-Calb2', 
'8'='SST-Crh',
'9'='SST-Myh8',
'10'='SST-Hpse',
'12'='SST-Mme',
'17'='SST-Nmbr',                                                  
'18'='SST-Nmbr',
'22'='SST-Syndig1l',                                                  
'24'='CHODL',
'27'='SST-Etv1',
'25'='Pv/Sst Th')
P28_hmap_v1 = subset(P28_sst, sherry_clusters %in% my_ord_v1)
P28_hmap_v1@meta.data$sherry_clusters = factor(droplevels(P28_hmap_v1@meta.data$sherry_clusters),
                                           levels=my_ord_v1, 
                                           ordered = T)