July 13, 2023

BICCN Data Dashboard Release

The consortium generated high value data for the neuroscience community from mouse, non-human primate and human species over five+ years. The data dashboard allows user to explore how much and what types of data were generated by the BICCN consortium scientists from 2018Q3-2023Q1.

July 10, 2023

Data Catalog Update and ABC Atlas Beta Release

The Data Catalog was updated with new data submitted by BICCN members through end of 2023 Q1.   Search the Data Catalog here.

The first release of Allen Brain Cell (ABC) Atlas [BETA] representing ~5,200 newly transcriptomic-defined cell types and their spatial locations across the whole mouse brain is live. This project uses data developed under BICCN and is integrated into the Data Catalog.   Read about the new product or access the visualization for these data here.

November 10, 2022

New Data: Data Catalog Update

This data release includes data submitted by BICCN members through end of 2022 Q3.   In this release we also added data citation language for ~20 projects and updated specimen counts and other minor changes. Search the Data Catalog here.

One new project was added in this release:

•     Cell type diversity in basal ganglia regions of human and non human primate [U01 Lein]

September 8, 2022

New Data: Data Inventory and Specimens

This data release includes data submitted by BICCN members through end of 2022 Q2.   In this release we included 5 new BICCN projects:

•     Mouse brain atlas common coordinate framework version 4: Nissl staining (U19 Huang)
•     Single-Cell Multi-Omic Analysis of the Developing Human Brain (U01 Kriegstein)
•     Spatial Transcriptomic Analysis of the Developing Human Brain (U01 Kriegstein)
•     Whole genome sequencing of the human basal ganglia  (U01 Macosko)
•     Collaboratory for atlasing cell type anatomy in the female and male mouse brain  (U01 Osten)

We also added searchable Specimen metadata with metadata and file manifest downloads for the following projects:

•     A Molecular and Cellular Atlas of the Marmoset Brain - Single nucleus sequencing (U01 Feng)
•     Transcriptomic cell types in the mouse brain: 10x cells (U19 Zeng)

May 10, 2022

New Data: Data Inventory

This data release includes information about BICCN data generated through Q1 2022. In this release we added 8 new BICCN projects:

• A compendium of cell-type specific isoform expression patterns across spatial and developmental axes. (RF1 Tilgner)
• Single-nucleus analysis of preoptic area development from late embryonic to adult stages. (U19 Huang)
• A molecularly defined and spatially resolved cell atlas of the mouses hypothalamus. (U19 Huang)
• Ultra-high Throughout Single Cell Multi-omic Analysis of Histone Modifications and Transcriptome in Mouse and Human Brains. (RF1 Ren)
• DNA methylation and chromatin conformation simultaneous profiling in individual human brain cell nuclei. (U01 Ecker)
• Cell type diversity in primary motor cortex across mammalian evolution. (Iso-seq; U01 Lein)
• Transcriptomic cell type characterization in human hippocampus. (U01 Lein)
• Human olfactory system - TempO-seq. (RF1 Shepherd)

December 15, 2021

New Data and New Features: Data Inventory and Specimens View

This data release includes information about BICCN data generated through Q3 2021 and includes data from >2800 brains and 37 million cells from 20 different species of mammals. An additional 18 data collections were added.  We have now added a “Browse Specimens” button for 2 BICCN projects that allows for search and filter of specimens based on their metadata. We will continue to add this feature to additional projects over time.

Project Summary pages were created for 6 new projects.

• Highly specific, renewable, and cost-effective antibody toolbox for 3D proteomic phenotyping of the brain (RF1 Chung)
• Developing Mouse Brain Imaging and Common Coordinate Framework (RF1 Kim)
• Human neocortical patch-seq (U01 Lein)
• Developmental cell census of human and non-human primate brain (U01 Sestan)
• A molecularly defined and spatially resolved projection atlas of the sensory neurons into the mouse main olfactory bulb (U19 Zeng)
• A 10X Multiome atlas of the primate and human basal ganglia (U01 Macosko)

August 31, 2021

New Data: Data Inventory and Project Summary pages

This data release includes updates to the BICCN data inventory deposited to data archives through Q2 2021 including more than 2,200 brains (and spinal cords) of imaging data, and >30 million cells of transcriptomic, epigenomic, electrophysiology and morphology data. New data was reported for for 12 new species, adding coverage of a variety of mammals beyond the original human, mouse, and marmoset.

Project Summary pages were created for 14 new projects. Note that data archive URLs will be added as they become available.

• Viral sparse labeling of connectionally-unique projection neurons for morphological assessment (U01 Dong)
• Single cell transcriptomic and epigenomic profile of the developing  mouse cortex (U19 Huang)
• Cell type diversity in primary motor cortex across mammalian evolution (U01 Lein)
• Multimodal analysis of human layer 5 pyramidal neurons (U01 Lein)
• A SHARE-seq atlas of the primate and human basal ganglia (U01 Macosko)
• A Slide-seq atlas of the primate and human basal ganglia (RF1 Macosko)
• A high-resolution molecular and lineage atlas of the mouse brain using Slide-seq (RF1 Macosko)
• Cross species M1 L5 ET comparison (U01 Lein)
• Single cell transcriptional and epigenomic atlas of the rhesus macaque brain (U01 Snyder-Mackler)
• Patch-clamp recording data from spinal cord neurons (U01 Zhang Li)
• A molecularly defined and spatially resolved cell atlas of the mouse main olfactory epithelium (U19 Zeng)
• MERFISH imaging of the mouse periaqueductal gray (U19 Huang)
• A molecularly defined and spatially resolved cell atlas of the mouse primary motor cortex (U19 Zeng)
• A molecularly defined and spatially resolved cell atlas of the mouse nucleus accumbens (U19 Huang)

June 7, 2021

New Data: Data Inventory and Project Summary pages

This data release documents updates to the inventory of BICCN data deposited at data archives through Q1 2021, including more than 2100 brains of imaging data, and over 25 million single cells of transcriptomic, spatial transcriptomic, epigenomic and morphology data.

New projects and data collections were added this quarter:

• 10xv2 transcriptomics data sets for periaqueductal gray and hypothalamus (U01 Huang – Dulac)
• Mesoscale connectivity data using retrograde transsynaptic tracing to understand input connectivity (U19 Huang)
• 10xv3 data for postnatal mouse brain development (RF1 Nowakowski)
• Single cell isoform expression across mouse brain development (RF1 Tilgner)
• 10xv3 data for mouse spinal cord (U01 Zhang, Li)
• 10xv3 data for mouse brain (U19 Huang – Macosko)
• Light sheet fluorescence microscopy 3D optical reconstruction of human brain tissue (U01 Fischl)
• Stereology of Broca and hippocampus (U01 Fischl)

December 15, 2020

New Data: Data Inventory and Project Summary pages

This data release contains BICCN data deposited at data archives through Q3 2020, for a total of 1794 brains and over 15 million single cells.

Changes and updates for data access:

• The Data Inventory and Project Summary pages have been re-released.

September 25, 2020

New Tool: Data Inventory and Project Summary pages

The Brain Cell Data Center provides access to the inventory of data generated by the BICCN consortium members. Our initial inventory report, the Cell Registry, is being replaced by a more user-friendly and extensible "Data Inventory". Now you can access information about the data-generating projects of the consortium and their respective data collections. There are many datasets from diverse experimental techniques, and more data is added regularly. New features allow you to search by experimental technique and species, which will make it easier for our community to find datasets of interest.  You can access this feature through the Data Access tab.

August 21, 2020

New Data: Cell Registry

The eighth BICCN data release contains data from 42 data sets generated by 15 grants. This quarter, 8 new datasets were submitted representing new modalities or new grants.

• Population Imaging: Brain-wide labeling patterns of enhancer viruses (RF1-Tasic)
• Epigenomics:
  • Chromatin accessibility data from mouse V1 (RF1-Tasic)
  • Chromatin accessibility profiling of genomic DNA in individual human brain nuclei (U01-Ecker)
  • DNA methylation profiling of genomic DNA in individual human brain cell nuclei (U01-Ecker)
• Genomics: DNA genome sequence of individual human brain donors (U01-Ecker)
• Anatomy:
  • Multi-resolution structural and diffusion MRI for the ex vivo whole human hemisphere (U01 Fischl)
  • Serial sectioning block-face polarization sensitive optical coherence tomography of ex vivo human brain blocks (U01 Fischl)
  • Light sheet microscopy of labeled whole mouse spinal cord (U01-Li Zhang)

June 24, 2020

New Data and Tools: Cell Registry and Transcriptomics Explorer

The seventh BICCN data release included the addition of five new datasets to the BICCN Cell Registry:

• Cell Morphology: Fluorescent in situ hybridization for marmoset (U01 Feng)
• Spatial Transcriptomics data: MERFISH (U19 Zeng and U19 Huang) and SeqFISH data (U01 Zhang, L)
• Multimodal: Patch-seq data (U19 Zeng)

New data was also added to existing datasets for an additional 132 brains, 128 sections and 1.1 million cells and nuclei, for a total count of BICCN data of 1,471 brains, 128 sections (spatial transcriptomics) and 11.2 million cells and nuclei.

Changes and updates for data access:

• Transcriptomics Explorer functionality has been continuously updated, and two new datasets were added in May and June 2020 generated using the 10x Chromium 3' sequencing platform.
  • Human motor cortex profiled as single nuclei (U01 Lein) profiled as single nuclei.
  • Mouse whole cortex and hippocampus profiled as single cells (U19 Zeng).
• Project Summary pages were removed as part of an infrastructure upgrade to improve user experience. This functionality will be provided in a future release.

February 6, 2020

New Data: Cell Registry

The sixth BICCN data release included the addition of seven new datasets to the BICCN Cell Registry:

• Cell morphology: MouseLight whole brain imaging data  in mouse (U19 Zeng)
• Transcriptomics: 10x Chromium 3’ sequencing v2 chemistry characterization of single nuclei in cortical projection neurons (U19 Huang)
• Transcriptomics: SMART-seq characterization of bulk sorted nuclei from cortical projection neurons (U19 Huang)
• Multimodal (Transcriptomics/Epigenomics): SNARE-seq
  • Split-seq data in marmoset (U01 Zhang, K)
  • Multimodal: ATAC-seq data in marmoset (U01 Zhang, K)
  • Multimodal: Split-seq data in human (U01 Zhang, K)
  • Multimodal: ATAC-seq data in human (U01 Zhang, K)

New data was also added to existing datasets for an additional 206 brains, and 1.6 million cells and nuclei.

This release brought the total count of BICCN data released to 1,339 brains and 10.1 million cells and nuclei.

October 15, 2019

New Data and Tool: Transcriptomics Explorer

The Transcriptomics Explorer enables researchers to visualize and analyze transcriptomics data and transcriptomic cell types for mouse and human, all directly in a web browser. The datasets currently made available for visualization and analysis include data generated under the U19 Zeng and U01 Lein BICCN grants.

New features are released regularly. Currently, researchers can:

• Explore a gene expression heatmap across cell types in the dataset, and search for genes of interest to inspect
• Explore a tSNE visualization of all cells in the dataset, colored by cell types or expression of genes of interest
• Visualize a dataset’s sampling strategy to see how cells and nuclei were sampled across brain areas, cortical layer, and other dimensions
• Find a cell type of interest in one visualization and examine its characteristics in a different visualization

The mouse dataset encompasses 75,000 single cells from multiple cortical areas and the hippocampus, providing the basis for comparative studies of cellular diversity in development, evolution, and diseases. This dataset includes SMART-seq v4 transcriptomics data generated under the U19 Zeng grant.

The human dataset encompasses 49,000 nuclei from multiple cortical areas, providing the basis for investigating the cellular diversity across human cortex and directly comparison of cell types with matched regions in mouse. This dataset includes SMART-seq v4 transcriptomics data generated under the U01 Lein grant.

New Data: Cell Registry

Two new datasets were added to the BICCN Cell Registry, including:

• Transcriptomics: 10x Chromium 3’ sequencing v2 chemistry data in mouse (U19 Zeng)
• Connectivity: TRIO transsynaptic tracing in mouse (U01 Dong)

Additionally, new data was added to existing datasets for an additional 196 brains, and 2.2 million cells and nuclei. Altogether, this release brought the total count of BICCN data released to 1,133 brains and 8.5 million cells and nuclei.

July 18, 2019

New Data: Cell Registry

The fourth BICCN data release included the addition of five new datasets to the BICCN Cell Registry:

• Epigenomics: single cell ATACseq data for developing human brain (U01 Kriegstein)
• Transcriptomics: 10x Chromium 3’ sequencing v3 chemistry data in mouse (U19 Zeng)
• Morphology: MORF confocal imaging data in mouse (U01 Yang)
• Morphology: reconstruction data from fMOST whole brain imaging in mouse (U19 Zeng)

Additionally, new data was added to existing datasets for an additional 103 brains, and 2.4 million cells and nuclei. Altogether, this release brought the total count of BICCN data released since August 2018 to 939 brains and 6.3 million cells and nuclei.

May 8, 2019

New Data and Tool: Cell Registry

The third BICCN data release included the launch of the Cell Registry. The Cell Registry features data indexing to enable data search and exploration. Users can filter available datasets by technique, species, investigator, grant, specimen type, or modality. The Cell Registry release represents a major infrastructural advancement from prior data access capabilities on the BICCN Portal, as all metadata is now served via API to access data from the Allen Institute for Brain Science Integrated Data Framework.
In addition to updates to existing BICCN datasets, the Cell Registry release included new Project Summary pages, which provide a deeper experimental context for the data in the Cell Registry. Project Summary pages allow enhanced metadata search, such as by anatomic region.  
Six Project Summary pages on transcriptomics and epigenomics projects were included in this release:

• DNA methylation profiling of genomic DNA in individual mouse brain cell nuclei (RS1.1)
• Chromatin accessibility profiling of genomic DNA in individual mouse brain cell nuclei (RS1.2)
• Transcriptomic cell types in the mouse brain: 10x cells
• Transcriptomic cell types in the mouse brain: 10x nuclei
• Transcriptomic cell types in the mouse brain: SMART-seq cells
• Transcriptomic cell types in the mouse brain: SMART-seq nuclei

December 12, 2018

New Data

The second BICCN data release via the BICCN Portal was in December 2018 and included an update to the counts of data deposited by the U01 and U19 data production grantees. This data represented a total of 544 brains, 2,644,600 cells and 8 distinct brain regions profiled by various methods.

August 23, 2018

New Data

The launch of the BICCN Portal in August 2018 supported the first public release of BICCN data. Primary data is available from the Brain Image Library (BIL) at the Pittsburgh Supercomputing Center and the Neuroscience Multi-Omic Archive (NeMO) at University of Maryland. The initial data release of the BICCN was served by a manually curated data access page, with linkages to the BIL and NeMO data archives for primary data access.

Altogether, 20 datasets were released with the launch of the BICCN Portal. These datasets were collected from human, non-human primate, and mouse, and encompassed multiple data modalities including transcriptomics, epigenomics, connectivity, cell morphology, and population imaging.