Human and Non-Human Primate Cell Atlas: Publication Package Highlights (Oct 26, 2023)

This webinar will focus on MapMyCells, a new interactive cell type taxonomy tool. MapMyCells enables users to upload their own cell type data and compare it to taxonomy datasets generated by the Allen Institute and their collaborators.

If you have any questions, please post them here: https://community.brain-map.org/

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This webinar will focus on the systematic classification of cell types and their hierarchical relationships. Similar to species taxonomy (family, genus, species, etc.), researchers at the Allen Institute and their collaborators are developing a standardized taxonomy for cell types.

If you are watching a recording of this webinar, please visit our community forum to submit your questions: https://community.brain-map.org/

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This webinar will focus on the Allen Brain Cell (ABC) Atlas, a platform for visualizing single-cell transcriptomic data in the brain. The atlas currently includes spatial, non-spatial, human, and mouse datasets. This webinar provides an introduction and general overview of the ABC Atlas and its features.

Please fill out this survey to help us better support your use of the ABC Atlas: https://www.surveymonkey.com/r/ABC_Atlas_Intro

If you have questions, please post them here: https://community.brain-map.org/

The Brain Initiative Cell Census Network (BICCN) is a collaborative consortium of many laboratories focused on understanding the cellular composition of the mammalian brain. BICCN has recently published a flagship paper describing the overall project, together with a companion collection of studies detailing the cell types, connectivity, anatomy, and other properties of the mammalian primary motor cortex (MOp, also known as M1).

This webinar presents multimodal research from leaders of several of the research teams involved in these efforts, providing insight into how diverse experimental approaches are being integrated to advance understanding of motor cortex organization and function.

Additional information is available at https://alleninstitute.org/what-we-do/brain-science/events-training/biccn-flagship-release

To read the Q&A and submit follow-up questions, please visit https://community.brain-map.org/t/decoding-the-mammalian-motor-cortex-biccn-flagship-release-webinar-q-a/1316

Learn about the Cell Types Knowledge Explorer (CTKE), a web tool that supports exploring individual cell types in M1.
See the tool at https://knowledge.brain-map.org/celltypes.

The human brain contains more than 100 billion cells, yet how these cells are organized into distinct types—and how those cell types vary across brain regions and species—remains an open question.

This webinar presents a new collection of studies focused on defining and characterizing the gene expression, gene regulatory, and morphoelectric features of cell types in the human and non-human primate brain. Using a range of cellular-resolution methods, most notably single-cell genomics, these studies mark the beginning of a new era of high-resolution analysis of the human and non-human primate brain. The implications for understanding human brain function, disease, and disease modeling are profound.

More information about the collection of studies is available at https://www.biccn.org/science/human-and-nhp-cell-atlas

Speakers and presentations:

Ed Lein, Allen Institute for Brain Science, 1:18

Kimberly Siletti, University Medical Center Utrecht, Netherlands, 5:12
Transcriptomic diversity of cell types in the adult human brain
http://www.science.org/doi/10.1126/science.add7046

Trygve Bakken, Allen Institute for Brain Science, 13:45
Comparative transcriptomics reveals human-specific cortical features
http://www.science.org/doi/10.1126/science.ade9516

Lijuan Liu, Southeast University, China, 22:40
Whole human-brain mapping of single cortical neurons for profiling morphological diversity and stereotypy
https://www.science.org/doi/10.1126/sciadv.adf3771

Wei Tian, Salk Institute, 32:17
Epigenomic complexity of the human brain revealed by single-cell DNA methylomes and 3D genome structures
http://www.science.org/doi/10.1126/science.adf5357

Chang Kim, University of California, San Francisco, 41:42
Spatiotemporal molecular dynamics of the developing human thalamus
http://www.science.org/doi/10.1126/science.adf9941

Q&A session, 51:32
Moderator: Yasmeen Hussain, Allen Institute for Brain Science

The research and webinar presented were funded by grants from the National Institutes of Health’s Brain Research Through Advancing Innovative Neurotechnologies® Initiative (The BRAIN Initiative). The publications were supported by and coordinated through the BRAIN Initiative Cell Census Network (BICCN) and the BRAIN Initiative Cell Atlas Network (BICAN).

The millions to billions of cells that comprise mammalian brains are organized into many highly specialized cell types. Previous studies have demonstrated that known and novel cell types can be identified by their single-cell gene expression profiles. However, the actual number of cell types in the brain and the degree of diversity among these cell types has remained unknown.

This webinar presents a new collection of studies from the BRAIN Initiative Cell Atlas Network (biccn.org), published in Nature on December 14, 2023, reporting the first complete cell type atlas of a mammalian brain. More than 30 million cells from the adult mouse brain were profiled using a combination of single-cell transcriptomic, epigenomic, and spatial transcriptomic approaches, identifying over 5,300 cell types across the entire mouse brain.

These studies uncover multiple organizing principles underlying the extraordinary diversity of cell types across the brain. This collective body of work represents a landmark achievement with far-reaching implications for understanding cell type–based brain circuit function across the neuroscience field.

More information about the collection of studies published in Nature on December 13, 2023 is available at https://www.biccn.org/science/whole-mouse-brain

Speakers and presentations:

1:21 Overview – Hongkui Zeng
https://www.biccn.org/science/whole-mouse-brain

6:20 A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain – Zizhen Yao
https://www.nature.com/articles/s41586-023-06812-z

17:38 Molecularly defined and spatially resolved cell atlas of the whole mouse brain – Xingjie Pan
https://www.nature.com/articles/s41586-023-06808-9

28:52 The molecular cytoarchitecture of the adult mouse brain – Jonah Langlieb
https://www.nature.com/articles/s41586-023-06818-7

38:40 Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain – Hanqing Liu
https://www.nature.com/articles/s41586-023-06805-y

51:59 Single-cell analysis of chromatin accessibility in the adult mouse brain – Songpeng Zu
https://www.nature.com/articles/s41586-023-06824-9

1:00:25 Brain-wide correspondence of neuronal epigenomics and distant projections – Jingtian Zhou
https://www.nature.com/articles/s41586-023-06823-w

1:11:01 A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons – Carla Winter
https://www.nature.com/articles/s41586-023-06817-8

1:22:10 Spatial atlas of the mouse central nervous system at molecular resolution – Hailing Shi
https://www.nature.com/articles/s41586-023-06569-5

1:32:49 Conserved and divergent gene regulatory programs of the mammalian neocortex – Ethan Armand
https://www.nature.com/articles/s41586-023-06819-6

1:43:34 Evolution of neuronal cell classes and types in the vertebrate retina – Karthik Shekhar
https://www.nature.com/articles/s41586-023-06638-9

1:54:21 Q&A session. Moderator: Yasmeen Hussain, Allen Institute for Brain Science

The research and webinar presented were funded by grants from the National Institutes of Health’s Brain Research Through Advancing Innovative Neurotechnologies® Initiative (The BRAIN Initiative). The publications were supported by and coordinated through the BRAIN Initiative Cell Atlas Network (BICCN) and the BRAIN Initiative Cell Atlas Network Infrastructure (BICAN).

The incredible complexity of the human brain poses enormous challenges in understanding how the brain underlies our thoughts and behaviors, and what goes wrong in disease. In addition, the inaccessibility of the human brain necessitates the use of closely related model organisms to study many aspects of brain structure and function that cannot be examined directly in humans. New, highly scalable technologies for studying individual cells based on the genes they express are rapidly advancing the field toward complete maps of the cell types that make up the brain. These methods also enable mapping of homologous cell types across species, helping to distinguish what can be studied in model organisms from what is unique to the human brain.

This webinar presents results from the BRAIN Initiative Cell Census Network (biccn.org), recently published in Science, describing the first draft of a brain-wide cell atlas of the adult human brain. Using single-cell RNA sequencing (single-cell transcriptomics), this work reveals exceptional diversity in brain cell types and their distribution across the brain, identifying more than 3,000 cell types. These cell atlasing efforts have now entered the next phase through the BRAIN Initiative Cell Atlas Network (BICAN), which focuses on humans and closely related non-human primate model organisms. These new initiatives integrate single-cell transcriptomics, epigenomics, and spatial transcriptomics to identify all cell types and map their spatial organization at both local tissue and larger-scale brain architectures.

These cell atlases are intended to serve as foundational community resources, similar in spirit to the Human Genome Project. Effective open-access tools are essential to realize the full potential of these resources to standardize and accelerate research across the field, enabling deeper understanding of brain function and disease. Tools for visualizing these data and for mapping user-generated datasets onto the atlases are also described.

Speakers and presentations:

03:39 – Ed Lein, Senior Investigator at the Allen Institute for Brain Science: Introduction and overview

15:20 – Kimberly Siletti, Assistant Professor at University Medical Center Utrecht
Transcriptomic cell-type diversity across the human brain
https://doi.org/10.1126/science.add7046

24:18 – Rebecca Hodge, Assistant Investigator at the Allen Institute for Brain Science
Building comprehensive cellular atlases of human and non-human primate brains using single-cell genomics
https://www.science.org/doi/10.1126/science.ade9516
https://www.science.org/doi/10.1126/science.adf2359
https://www.science.org/doi/10.1126/science.adf6812

32:28 – Stephanie Seeman, Scientist at the Allen Institute for Brain Science
https://www.science.org/doi/10.1126/science.ade9516
https://www.science.org/doi/10.1126/science.adf6812

41:30 – Elysha Fiabane, Product Manager at the Allen Institute for Brain Science
Web tools for visualizing and analyzing human and mammalian brain atlases
https://knowledge.brain-map.org/celltypes
https://portal.brain-map.org/atlases-and-data/bkp/abc-atlas
http://knowledge.brain-map.org/mapmycells/process/

41:30 – Q&A session

Moderator:
Jimena Garcia, Program Manager, Inclusive Research, Allen Institute

More information about Human and Mammalian Brain Atlas (HMBA) efforts, including links to papers and datasets, is available at https://www.biccn.org/science/human-and-nhp-cell-atlas and https://www.portal.brain-bican.org/.

We appreciate your engagement with this webinar and look forward to connecting with you again at future events listed at brain-bican.org/events.

This webinar was supported by the BRAIN Initiative Cell Atlas Network (BICAN) of the National Institutes of Health under the Human and Mammalian Brain Atlas (HMBA) Consortium, award number UM1MH130981. The publications were supported by and coordinated through the BRAIN Initiative Cell Census Network (BICCN) and BRAIN Initiative Cell Atlas Network (BICAN).