Single Cell Analysis (Systems Biology)

Overview of Services

The Single Cell Analysis Core is housed in the Sulzberger Columbia Genome Center and provides experimental and computational support for single-cell RNA-Seq (scRNA-Seq). The Core was launched with generous support from the Columbia Precision Medicine Initiative, the Irving Institute for Clinical and Translational Research, the Herbert Irving Comprehensive Cancer Center, and the Department of Medicine.

The 10x Genomics Single Cell Gene Expression 3’ and 5’ workflows are both high-throughput, scalable technologies that encapsulate thousands of individual cells (or nuclei) in droplets for lysis and reverse transcription from up to 8 samples in parallel. The droplets contain primers for cell- and and molecule-specific barcoding of cDNA. We can prepare libraries for CITE-Seq/feature barcoding, CRISPR, or cell hashing. Using our 5’ workflow, we can profile the full length V(D)J regions from T-cell or B-cell receptors from human and mouse samples. The resulting libraries are typically sequenced on an Illumina NovaSeq 6000. Users must deliver live cells (or nuclei) in suspension to the Core.

 The 10x Genomics Single Cell ATAC workflow is a comprehensive, scalable approach to determine the regulatory landscape of chromatin in thousands of cells in a single sample. Nuclei are delivered in suspension to the Core, then transposed in bulk before being encapsulated in droplets for individual nuclei barcoding. The resulting libraries are typically sequenced on an Illumina NextSeq 500/550.

 The 10x Genomics Multiome ATAC + Gene Expression workflow simultaneously profiles the epigenomic landscape and gene expression in the same single nuclei for thousands of nuclei in parallel. As above, nuclei are transposed in bulk to add adapters to the ends of the DNA before being encapsulated in droplets. The droplets contain reagents and beads with a poly(dT) sequence that enables production of barcoded, full-length cDNA from poly-adenylated mRNA for gene expression (GEX) library and a Spacer sequence that enables barcode attachment to transposed DNA fragments for ATAC library. Resulting libraries are typically sequenced on an Illumina NovaSeq 6000 or a NextSeq 500/550.

All first-time users are required to schedule an in-person meeting to discuss projects, please contact genome@colubmia.edu to schedule a meeting.

Leadership

Name Role Phone Email Location
Peter Sims Faculty Director pas2182@cumc.columbia.edu Lasker 203
Erin Bush Director   genome@columbia.edu  Lasker 208
Izabela Krupska Senior Staff Associate genome@columbia.edu  Lasker 208
Lucy Anisimov Staff Associate genome@columbia.edu Lasker 208
Nicola Solares Bioinformatics Analyst genome@columbia.edu Lasker 208

 

Location and hours of operation

Hours Location

Monday - Friday     

9 AM - 5 PM  

3960 Broadway, Lasker 208

New York, NY 10032

Links and Resources

Contacts

Name Role Phone Email Location
Erin Bush
Director
 

 
genome@columbia.edu
 
Lasker 208