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The BRAIN Initiative Cell Atlas Network (BICAN) is committed to rapid data sharing to increase the accessibility and impact of data generated by its members. Through a federated pipeline for metadata collection, sequencing, and data processing, BICAN enables unpublished data that has completed basic quality control to be made available to the research community.
This third public release of post-QC single-cell and single-nucleus transcriptomic and epigenomic data from BICAN is the first to include processed data files (aligned data, counts, and analysis metrics) from BICAN’s common sequencing analysis pipelines. It spans 9 institutions, 1,018 donors, 10,248 specimens (library aliquots), and 74 data collections.
Data are accessible through NIMP and the NeMO archive, linked to the Data Catalog by shared metadata and identifiers. Licenses are CC-BY (non-human), BICAN-BY-NR (open-access human), or other data use agreements (controlled-access human).
Data is further packaged into 74 “collections” of files available individually through the Neuroscience Multi-omic Archive (NeMO); each collection is grouped by technique, species, grant, participating laboratory, and data use restriction. New in this release are 34 raw sequencing collections, from human Paired-Tag data (Ren lab, UC San Diego) to mouse locus ceruleus, spinal cord, and developmental data (Cohen, Lai, and Arlotta labs), plus collections from the Lein, Krienen, and McCarroll labs. It also adds 24 processed datasets from 10x Chromium 3' (v3.1/v3.1-HT and v4), 10x Multiome RNA-seq, and snm3C-seq pipelines, which include BAM files, cellxgene matrices and other metrics files. Existing collections were also updated from eight labs across seven institutions.
General Licensing and Usage Guidelines
Data in this release are provided under different licenses. Users should review the Data Catalog collection entries and the README file available for download alongside specimen and file manifests for the applicable license for each dataset.
In general, non-human datasets are made available under a CC-BY-4.0 license. Human data derived from tissue consented for open access are provided under BICAN-BY-NR. Human controlled access data is shared on approval and subject to consent restrictions - see the NeMO documentation on access controls for further information.
When reusing data, please provide attribution to the data generators by citing the appropriate data citation. Data citations can be found with the collection at the NeMO archive or in the Data Catalog collection entries.
Rapid release files are provided in a raw state. FASTQ files are split by sequencing lane, so each library aliquot has multiple files, and a single library may have more than one sequenced aliquot. BAM files are organized the same way. Users will need to merge the appropriate files themselves; keeping them separate allows quality control to be repeated on each file before merging.
Data in the rapid release were generated by multiple laboratories as part of the BRAIN Initiative Cell Atlas Network. New to this release are collections of multi-modal human data from the Luo lab at the University of California, Los Angeles, developmental mouse data from the Arlotta lab at Harvard University, and multi-modal data from lemur, mole-rat, and pig-tailed macaque from the Allen Institute (Lein). This release also has updates to existing collections including developmental mouse data from the Allen Institute (Zeng) and University of California, San Francisco (Nowakowski), cross-species data from the Allen Institute (Lein), marmoset data from Princeton University (Krienen), as well as human transcriptome data from the Broad Institute (McCarroll) and epigenomic data from the Salk Institute (Ecker). The NIH grant awards contributing to data in this initial release are shown below.
Data Contributors:
The data ecosystem that supports the rapid release includes three platforms: the Brain Knowledge Platform (BKP; Allen Institute for Brain Science), the Neuroanatomy-anchored Information Management Platform for Collaborative BICAN Data Generation (NIMP, RRID:SCR_024684; The University of Texas Health Science Center at Houston) and the fastq file storage at NeMO archive. These integrated platforms will continue to enable regular cross-consortium data releases going forward.
Metadata and resource identifiers (NHash, RRID:SCR_025313) for specimens and sequencing data are captured, managed, and cross-linked through NIMP (RRID:SCR_024684) for Collaborative BICAN Data Generation, codifying critical BICAN data standards and standard operating processes to ensure trackable experimental workflow and data integrity for down-stream data archives of the entire BICAN consortium.
Single cell omics data processing pipelines were developed by the Broad Data Sciences Platform in partnership with the BICAN community. Pipelines are available on GitHub (RRID:SCR_002630), Dockstore, and the cloud workbench Terra (RRID:SCR_021648) Data operations (including data ingestion, storage, and release) are performed by the Neuroscience Multi-omic (NeMO) Archive team at the University of Maryland.
The following NIH Awards provided infrastructure support for this Rapid Release of single-cell omics data.
Single-cell Omics infrastructure contributors