Advances in genomic technologies have made it possible to characterize molecular profiles, such as the transcriptome or epigenome, of individual cells. The discovery of rare but important cell types, delineation of cell trajectories in development, and the importance of cell type proportions in health and disease are among the many discoveries enabled by these technological advances. While many commercial single-cell molecular profiling technologies are available, they remain prohibitively expensive for large-scale projects. To address this limitation, single cell combinatorial indexing (sci-) based methods were developed. Sci-based methods leverage a ‘split and pool’ molecular barcoding strategy to enable exponentially large numbers of nuclei to be molecularly profiled at a low cost-per-cell, albeit at a high cost-per-experiment.

Single Cell Genomics

By performing large-scale single cell molecular profiling experiments in a centralized lab, we aim to produce high quality, consistent data while keeping costs for individual researchers to a minimum. The BBI Advanced Technology Lab (BAT-Lab) currently offers services for two molecular profiling technologies: optimized sci-RNA-seq3 and sci-ATAC-seq3. Services range from in-house tissue dissociation and nuclei isolation (optional), through single-cell sequencing and basic data analysis. Of note, we currently perform sci-experiments only on fixed nuclei, and the sci-RNA-seq is a polyA capture based method (3’-end counting). Both raw sequencing and analysis-ready data (demultiplexed, cell by gene count matrices) are returned, along with helpful QC and preliminary analyses. See below for more information about our bioinformatics services and support.

Our pricing structure depends on the number of samples, whether the sample prep is to be performed in house (i.e. nuclei isolation), which technology is requested, and the targeted number of nuclei to be sequenced. Please contact us at sci-help@brotmanbaty.org to discuss your project and our current rates.

For more information and bioinformatics training support, please visit the Brotman Baty Institute website for more details

SCI-Based Services

Projects

In working with the Seattle Hub for Synthetic Biology, the overarching goal of the Single-Cell team is to provide the single-cell expertise to enable the systematic mapping of the conserved genetic program controlling vertebrate embryogenesis by disrupting genes and pathways in developmental models.

Current projects include:

Produce a reference atlas across vertebrates

  • Generate time-resolved transcriptomic and epigenomic atlas of zebrafish development from 6 hours post-fertilization to 28 days post-fertilization

  • Generate time-resolved transcriptomic atlases of human and mouse gastrulation models from 0-120 hours.

Produce a perturbation atlas across vertebrates

  • Transcriptionally profile at least 5M single cells from thousands of zebrafish embryos and mouse and human gastruloids that have been treated with small molecule, chemical inhibitors

  • Transcriptionally profile at least 20M single cells from thousands of zebrafish embryos and mouse and human gastruloids that have been genetically perturbed at strategically selected loci.