RNA-Seq Data from Allen Brain Atlas (ABA) Source: https://portal-brain-map.org/atlases-and-data/rnaseq/

This data set includes single cell and nuclear transcriptomic profiles, assayed from human brain regions. Anatomical specificity is achieved by microdissecting tissue from defined brain areas, such as cortical layers or cell groups in LGd.

Towards that goal, ABA scientists have generated a dataset that includes close to 75,000 single cells from multiple cortical areas and the hippocampus. Samples were collected from fine dissections of brain regions from male and female mice. For most brain regions, they isolated labeled cells from pan-GABAergic, pan-glutamatergic, and pan-neuronal transgenic lines. For primary visual cortex (VISp) and anterolateral motor cortex (ALM), they sampled additional cells using driver lines that label more specific and rare types.

To investigate the correspondence between transcriptomic types and neuronal projection properties, we collected cells labeled from retrograde injections for select combinations of target injection sites and dissection regions. Labeled cells were collected by fluorescence activated sorting (FACS) of single cells. We also collected cells without fluorescent label to sample non-neuronal cell types. Isolated single cells were processed for RNA sequencing using SMART-Seq v4. This dataset reveals the molecular architecture of the neocortex and hippocampal formation, with a wide range of shared and unique cell types across areas. It provides the basis for comparative studies of cellular diversity in development, evolution, and diseases.

Detailed protocols describing experimental methods and analysis steps are described in the Transcriptomics Overview technical whitepaper (http://help.brainmap.org/download/attachments/8323525/CellTypes_Transcriptomics_Overview.pdf. )

Additional RNA-Seq data generated as part of the Brain Initiative Cell Census Network (BICCN) from ABA is available as part of the Brain Cell Data Center (BCDC) portal.

Gene Expression data by Cluster, median were downloaded from https://portal.brain-map.org/atlases-and-data/rnaseq. The expression values were normalized using the expression of Gapdh as 100. GeneID, synonyms and descriptions were added to each gene symbol of the ABA median output. The cell population was sorted into inhibitory (expression of Slc32a1), excitatory (expression of Slc17a7 and Nrn1) and other cell types. The expression values could be obtained by search under geneID, gene symbol, synonyms or gene descrition.

Helps from Dr. Lee Eiden and Dana Bakalar for cell sorting are greatly appreciated.

Babru Samal