HCA Data Explorer

Conserved cell types with divergent features in human versus mouse cortex.

Updated August 30, 2022

Elucidating the cellular architecture of the human cerebral cortex is central to understanding our cognitive abilities and susceptibility to disease. Here we used single-nucleus RNA-sequencing analysis to perform a comprehensive study of cell types in the middle temporal gyrus of human cortex. We identified a highly diverse set of excitatory and inhibitory neuron types that are mostly sparse, with excitatory types being less layer-restricted than expected. Comparison to similar mouse cortex single-cell RNA-sequencing datasets revealed a surprisingly well-conserved cellular architecture that enables matching of homologous types and predictions of properties of human cell types. Despite this general conservation, we also found extensive differences between homologous human and mouse cell types, including marked alterations in proportions, laminar distributions, gene expression and morphology. These species-specific features emphasize the importance of directly studying human brain.

Ed S LeinAllen Institute for Brain Scienceedl@alleninstitute.org
Rebecca D Hodge1
Trygve E Bakken1
Jeremy A Miller1
Kimberly A Smith1
Eliza R Barkan1
Lucas T Graybuck1
Jennie L Close1
Brian Long1
Nelson Johansen2
Osnat Penn1
Zizhen Yao1
Jeroen Eggermont3
Thomas Höllt3
Boaz P Levi1
Soraya I Shehata1
Brian Aevermann4
Allison Beller5
Darren Bertagnolli1
Krissy Brouner1
Tamara Casper1
Charles Cobbs6
Rachel Dalley1
Nick Dee1
Song-Lin Ding1
Richard G Ellenbogen7
Olivia Fong1
Emma Garren1
Jeff Goldy1
Ryder P Gwinn6
Daniel Hirschstein1
C Dirk Keene5
Mohamed Keshk4
Andrew L Ko7
Kanan Lathia1
Ahmed Mahfouz3
Zoe Maltzer1
Medea McGraw1
Thuc Nghi Nguyen1
Julie Nyhus1
Jeffrey G Ojemann7
Aaron Oldre1
Sheana Parry1
Shannon Reynolds1
Christine Rimorin1
Nadiya V Shapovalova1
Saroja Somasundaram1
Aaron Szafer1
Elliot R Thomsen1
Michael Tieu1
Gerald Quon2
Richard H Scheuermann4
Rafael Yuste8
Susan M Sunkin1
Boudewijn Lelieveldt3
David Feng1
Lydia Ng1
Amy Bernard1
Michael Hawrylycz1
John W Phillips1
Bosiljka Tasic1
Hongkui Zeng1
Allan R Jones1
Christof Koch1
Ed S Lein1
1Allen Institute for Brain Science
2University of California
3Leiden University Medical Center
4J. Craig Venter Institute
5University of Washington
6Swedish Neuroscience Institute
7University of Washington School of Medicine
8Columbia University
Irene Pérez-Díez

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/165dea71-a95a-44e1-88cd-b2d9ad68bb1e

Supplementary links are provided by contributors and represent items such as additional data which can’t be hosted here; code that was used to analyze this data; or tools and visualizations associated with this specific dataset.

1.http://celltypes.brain-map.org/2.http://data.nemoarchive.org/biccn/grant/u01_lein/lein/transcriptome_tbc/scell/SMARTseq/processed/counts/3.http://portal.brain-map.org/4.https://identifiers.org/dbgap:phs001790
None

Downloaded and exported data is governed by the HCA Data Release Policy and licensed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). For more information please see our Data Use Agreement.

Analysis Portals

None

Project Label

conservedCellTypesHumanMouse

Species

Homo sapiens

Sample Type

specimens

Anatomical Entity

brain

Organ Part

left cerebral hemisphere

Selected Cell Types

2 cell types

Disease Status (Specimen)

normal

Disease Status (Donor)

normal

Development Stage

human adult stage

Library Construction Method

Smart-seq

Nucleic Acid Source

single nucleus

Paired End

true

Analysis Protocol

ap_rawMatrix

File Format

3 file formats

Cell Count Estimate

49.4k

Donor Count

3
.csv1 file(s)csv1 file(s)xlsx1 file(s)