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. We are excited to provide services using two scRNA-Seq platforms: the 10x Genomics Chromium 3' Solution and pooled scRNA-Seq in 96-well plates.

 

The 10x Genomics Chromium Single Cell 3' Solution is a high-throughput, scalable technology that encapsulates thousands of individual cells 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. The resulting pooled, 3'-end libraries are typically sequenced on a NovaSeq 6000. Users must deliver live cells in suspension to the Core.

 

For scRNA-Seq in 96-well plates, users sort individual cells into the wells of a 96-well plate containing lysis buffer (provided by the Core). This step is performed at the user's convenience. After sorting, plates are spun down, frozen, and delivered to the Core where they are processed with our automated liquid handling robot. Template-switching reverse transcription is performed with adapter-linked oligo(dT) primers containing both cell- and molecule-specific barcodes, and cDNAs are pooled for PCR and library construction. Pooled, 3'-end sequencing libraries are then sequenced on an Illumina NextSeq 500. At least two plates are required per project.

 

The two methods provide different levels of throughput and flexible options. All first-time users are required to schedule an in-person meeting to discuss projects with Peter Sims and Erin Bush (genome@columbia.edu).

Leadership

Name Role Phone Email Location
Peter Sims Director 212 305 2687 pas2182@cumc.columbia.edu Lasker 203
Erin Bush Associate Director 212 305 1572 ecb2152@cumc.columbia.edu Lasker 208
Michael Finlayson Bioinformatics Analyst 212 305 1572 mf3189@cumc.columbia.edu Lasker 208
Izabela Krupska   212 305 1572 ik2372@cumc.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
Associate Director
 
212-305-1572
 
ecb2152@cumc.columbia.edu
 
Lasker 208