Data Releases

 

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:

 

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.