Annotations for V1 single-cell transcriptomic datasets

A dataset consisting of descriptive annotation data for 3357 of the nuclei characterized in Hodge, et al. (2019). These metadata are subset to 50 cells per donor to fit in GitHub. Metadata for the complete set of nuclei is available at brain-map.org.

metadata_Hodge2019

Format

A Data Frame with 141 columns and 3357 rows

sample_name

An ID that uniquely corresponds to a single cell. Matches column names in data_Hodge2019 and rownames in metadata_Hodge2019

cluster_label

The primary cluster assigned to each cell. Matches the labels in dend_Hodge2019

cluster_id

ID number for the primary cluster assigned to each cell, corresponding to cluster order in the dendrogram

cluster_color

Color for the primary cluster assigned to each cell

subclass_label

Intermediate classification of cell types. Subclasses were defined after publication based on matching between human MTG (Hodge et al 2019) and both human M1 (Bakken et al 2021) for most cells types and mouse VISp (Tasic et al 2018) in a few edge cases. Names and within-class order conform with other Allen Institute taxonomies

subclass_id

ID number for the subclass assigned to each cell, corresponding to cluster order in the dendrogram

subclass_color

Color for the subclass assigned to each cell

class

Broad classification of cell types into GABAergic, glutamatergic, and non-neuronal

cell_roi

Specific region of interest (roi) of the collected cells in the form (brain region)_(cortical layer)

average_layer

Average cortical layer of all cells in a cluster

donor_name

External identifier corresponding to individual donors

donor_age_yrs

Donor age in years

donor_sex

Sex of the donor: (M)ale, (F)emale, or unknown

hemisphere

Which hemisphere the tissue was collected from

species

Homo sapiens for all nuclei

total_reads

Total number of reads as reported from the alignment