column_name,column_description
sample_id_anon,anonymised ID for sample
individual_id_anon,anonymised ID for donor
cell_id,"id for cell, corresponding to the column names of the counts matrix (this is sample_id plus droplet barcode)"
type_fine,fine cell type annotation
type_broad,broad cell type annotation
cluster_zoom,"cluster used to define type_fine (type_broad was determined by clustering at the whole experiment level, subsets of the data were then clustered, and this was used to define type_fine; cluster_zoom indicates both the subset that was used, and the clusters within that subset)"
exclude_pseudobulk,TRUE if this cell was excluded from the pseudobulk analysis; this indicates that the cluster appeared to be mixed based on the expression of marker genes
cortical_layer,annotations of cortical layers for a subset of neuronal cell types; this is used to account for differences in layers in GM
log10_counts,log10 library size for this barcode
log10_feats,log10 number of genes observed for this barcode
logit_mito,logistic function of proportion of mitochondrial genes for this barcode (in R: qlogis(pct_mito/100))
logit_splice,logistic function of proportion of spliced genes for this barcode (in R: qlogis(pct_splice/100))
pct_mito,percentage of mitochondrial genes for this barcode
pct_splice,percentage of spliced genes for this barcode
lesion_type,"lesion type for this sample (WM = ctrl WM, NAWM = normal appearing WM, AL = active lesion, CAL = chronic lesion, CIL = chronic inactive lesion, RL = remyelinating lesion, GM = ctrl GM, NAGM = normal appearing GM, GML = cortical lesion)"
seq_pool,randomly allocated pool of samples to be sequenced together
matter,white matter (WM) or grey matter (GM)
sample_source,brain bank of origin for this sample
diagnosis,"MS diagnosis for this donor (CTR = non MS, SPMS = secondary progressive MS, PPMS = primary progressive MS, RRMS = relapsing remitting MS)"
sex,male or female (checked against expression of known X- and Y-linked genes)
age_at_death,"age at death, in years"
cause_of_death,cause of death
years_w_ms,number of years with MS
pmi_minutes,"post-mortem interval, in minutes"
smoker,"smoking status of donor, where known (smoker, non-smoker, cannabis smoker, unknown)"
age_scale,"age at death, scaled across donors to have mean 0 and standard deviation 0.5 (see Gelman 2008)"
age_cat,"age categorised into below 50, over 70 and between"
pmi_cat,"pmi_minutes categorised into up to 6 hours, 6 hours to 12 hours, and 12 hours or more"
pmi_cat2,"pmi_minutes categorised into up to 12 hours, and 12 hours or more (necessary for using pmi_cat to model GM, where only one sample had pmi_cat up to 6 hours)"