Identifiers

Identifier Results

Field Value
Identifier nemo:dat-rg2rc5m
Dataset Name Transcriptomic cytoarchitecture reveals principles of human neocortex organization
Version NA
Release Date NA
DOI NA
Source Data URL NA
Dataset Collection URL
Description Variation in cortical cytoarchitecture is the basis for histology-based definition of cortical areas, such as Brodmann areas. Single cell transcriptomics enables higher-resolution characterization of cell types in human cortex, which we used to revisit the idea of the canonical cortical microcircuit and to understand functional areal specialization. Deeply sampled single nucleus RNA-sequencing of eight cortical areas spanning cortical structural variation showed highly consistent cellular makeup for 24 coarse cell subclasses. However, proportions of excitatory neuron subclasses varied strikingly, reflecting differences in intra- and extracortical connectivity across primary sensorimotor and association cortices. Astrocytes and oligodendrocytes also showed differences in laminar organization across areas. Primary visual cortex showed dramatically different organization, including major differences in the ratios of excitatory to inhibitory neurons, expansion of layer 4 excitatory neuron types and specialized inhibitory neurons. Finally, gene expression variation in conserved neuron subclasses predicts differences in synaptic function across areas. Together these results provide a refined cellular and molecular characterization of human cortical cytoarchitecture that reflects functional connectivity and predicts areal specialization.
Keywords human, cortex, snRNA-seq, SSv4, cross-areal
Total Files in Collection 152897
Total Size in Collection (in GB) 20549.1
Authors Nikolas L. Jorstad, Jennie Close, Nelson Johansen, Anna Marie Yanny, Eliza R. Barkan, Kyle J. Travaglini, Darren Bertagnolli, Jazmin Campos, Tamara Casper, Kirsten Crichton, Nick Dee, Song-Lin Ding, Emily Gelfand, Jeff Goldy, Daniel Hirschstein, Matthew Kroll, Michael Kunst, Kanan Lathia, Brian Long, Naomi Martin, Delissa McMillen, Trangthanh Pham, Christine Rimorin, Augustin Ruiz, Nadiya Shapovalova, Soraya Shehata, Kimberly Siletti, Saroja Somasundaram, Josef Sulc, Michael Tieu, Amy Torkelson, Herman Tung, Katelyn Ward, Edward M. Callaway, Patrick R. Hof, C. Dirk Keene, Boaz P. Levi, Sten Linnarsson, Partha P. Mitra, Kimberly Smith, Rebecca D. Hodge, Trygve E. Bakken, Ed S. Lein
Organization Allen Institute for Brain Science
Contact Person Ed S. Lein, Trygve E.Bakken, Rebecca D. Hodge
Contact E-Mail edl@alleninstitute.org, trygveb@alleninstitute.org, rebeccah@alleninstitute.org
External Identifier
Grant Name U01MH114812, U19MH114830
Consortium BICCN
Data Repository NeMO
Data Repository RRID RRID:SCR_016152
Data License controlled access data subject to data use certification
Data Access
Community Standards
Study Organism human
Protocol ID dx.doi.org/10.17504/protocols.io.bf4ajqse; dx.doi.org/10.17504/protocols.io.bq6ymzfw; dx.doi.org/10.17504/protocols.io.ewov149p7vr2/v2; dx.doi.org/10.17504/protocols.io.bq64mzgw; dx.doi.org/10.17504/protocols.io.774hrqw; dx.doi.org/10.17504/protocols.io.8epv517xdl1b/v2; dx.doi.org/10.17504/protocols.io.brdjm24n; dx.doi.org/10.17504/protocols.io.bq7cmziw
Field Value
Identifier
Description Controlled, raw 10x data from Layer 5 (L5) of human cortex, generated by the Lein lab, associated with the following publication: Jorstad et al, 2022. Transcriptomic cytoarchitecture reveals principles of human neocortex organization. bioRxiv doi.org/10.1101/2022.11.06.515349
Source Data URL This is a restricted access dataset. Instructions for controlled access are available at https://nemoarchive.org/resources/accessing-controlled-access-data.php
Field Value
Identifier
Description Open, raw 10x data from the Middle Temporal Gyrus (MTG) of humans, generated by the Lein lab, associated with the following publication: Jorstad et al, 2022. Transcriptomic cytoarchitecture reveals principles of human neocortex organization. bioRxiv doi.org/10.1101/2022.11.06.515349
Source Data URL
Field Value
Identifier
Description Controlled, raw SSv4 data from Middle Temporal Gyrus (MTG) of humans, generated by the Lein lab, associated with the following publication: Jorstad et al, 2022. Transcriptomic cytoarchitecture reveals principles of human neocortex organization. bioRxiv doi.org/10.1101/2022.11.06.515349. This dataset is included within NDA Permissions Group 'BRAIN/NeMO: A multimodal atlas of human brain cell types: Human Cortex, BRAIN/NeMO: A multimodal atlas of human brain cell types: Middle Temporal Gyrus (MTG)'.
Source Data URL This is a restricted access dataset. Instructions for controlled access are available at https://nemoarchive.org/resources/accessing-controlled-access-data.php
Field Value
Identifier
Description Controlled, raw SSv4 data from human cortex, associated with the following publication: Jorstad et al, 2022. Transcriptomic cytoarchitecture reveals principles of human neocortex organization. bioRxiv doi.org/10.1101/2022.11.06.515349. This dataset is included within NDA Permissions Group 'BRAIN/NeMO: A multimodal atlas of human brain cell types: Human Cortex RNASeq'
Source Data URL This is a restricted access dataset. Instructions for controlled access are available at https://nemoarchive.org/resources/accessing-controlled-access-data.php
Field Value
Identifier
Description Controlled, processed SSv4 data from Middle Temporal Gyrus (MTG) of humans, generated by the Lein lab, associated with the following publication: Jorstad et al, 2022. Transcriptomic cytoarchitecture reveals principles of human neocortex organization. bioRxiv doi.org/10.1101/2022.11.06.515349. This dataset is included within NDA Permissions Group 'BRAIN/NeMO: A multimodal atlas of human brain cell types: Human Cortex, BRAIN/NeMO: A multimodal atlas of human brain cell types: Middle Temporal Gyrus (MTG)'.
Source Data URL This is a restricted access dataset. Instructions for controlled access are available at https://nemoarchive.org/resources/accessing-controlled-access-data.php
Field Value
Identifier
Description Controlled, processed SSv4 data from human cortex, associated with the following publication: Jorstad et al, 2022. Transcriptomic cytoarchitecture reveals principles of human neocortex organization. bioRxiv doi.org/10.1101/2022.11.06.515349. This dataset is included within NDA Permissions Group 'BRAIN/NeMO: A multimodal atlas of human brain cell types: Human Cortex RNASeq'.
Source Data URL This is a restricted access dataset. Instructions for controlled access are available at https://nemoarchive.org/resources/accessing-controlled-access-data.php
Field Value
Identifier
Description Analysis bag contains open processed data associated with the following publication: Jorstad et al, 2022. Transcriptomic cytoarchitecture reveals principles of human neocortex organization. bioRxiv doi.org/10.1101/2022.11.06.515349
Source Data URL
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