Fluidigm Corporation today announced the availability of Single-Cell ATAC-seq, an epigenetics application for the C1TM system, that allows researchers to explore the regulatory systems that drive cellular function. This application is freely available to researchers on Script Hub™, a new web portal within Fluidigm’s C1 Open AppTM program.
As described in a paper just published in Nature entitled “Single-cell chromatin accessibility reveals principles of regulatory variation” by Jason D. Buenrostro, William J. Greenleaf, Howard Chang et.al., the researchers use ATAC-seq to identify single-cell DNA accessibility profiles from diverse cell types. Understanding the accessible regions of the genome will reveal the role of DNA-binding proteins, nucleosomes, and chromatin compaction in regulating gene expression. Until now, researchers needed at least 500 cells to identify accessible chromatin regions, which misrepresented the heterogeneity present in the biological system.
“We believe scATAC-seq will enable the interrogation of the epigenomic landscape of small or rare biological samples allowing for detailed, and potentially de novo, reconstruction of cellular differentiation or disease at the fundamental unit of investigation – the single cell,” said William J. Greenleaf, Ph.D., Principal Investigator, Greenleaf Lab and Assistant Professor, Department of Genetics, Stanford University.
“We designed the C1 to be very flexible. The Open App program is an ecosystem between method development laboratories and our cell biology users. We created this program to give our users maximum flexibility to expand their capability and experimental strategy over time and to showcase creativity. We’re thrilled to see the C1 community come together and pioneer the next frontier of single-cell biology: single-cell epigenetics,” said Candia L. Brown, Fluidigm Single-Cell Genomics Business Director of Product Marketing.
Co-developed by the Greenleaf Lab, the Chang Lab and Fluidigm, ATAC-seq is now available on Script Hub for use with the C1 Open App IFC. The C1 Open App program is comprised of Script Hub, C1 Script Builder™, the Open App IFC, and the Open App Reagent Kit. These tools give researchers the ability to create and share the latest single-cell applications with other C1 users.
Single-Cell ATAC-seq is the first method to be published and shared on Script Hub. Other user-developed applications available on Script Hub include:
- Single-Cell CEL-seq: developed by Itai Yanai, Israel Institute of Technology
- Single-Cell STRT-seq: developed by Sten Linnarson, Karolinska Institute
- LPS Stimulation: developed by the Regev Lab, Broad Institute, and Fluidigm
Apps on Script Hub are freely available to the C1 community and are compatible with any C1 system. Each application includes the script, protocol, reference data and links to publications. All registered Script Hub users can rate and comment on published applications.