Peter A. Sims, Director

Erin C. Bush, Associate Director

Jake Hagen, Bioinformatics Analyst


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 in one lane of an Illumina HiSeq 4000. 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 (


In addition to the capital equipment assets in the Sulzberger Columbia Genome Center, the Single Cell Analysis Core maintains the following instruments:

10x Genomics Chromium Single Cell Controller

Beckman-Coulter Biomek 4000

ThermoFisher Countess II FL Automated Cell Counter

Miltenyi gentleMACS Octo Dissociator (available for self-service use, please contact for scheduling)


We recognize that scRNA-Seq presents numerous analytical challenges, and that computational techniques in this area are rapidly evolving. We are therefore pleased to provide bioinformatics support for processing, quality control, analysis, and interpretation of scRNA-Seq data generated by the core as part of the service packages listed below. In addition to basic data processing (barcode demultiplexing, alignment, molecular counting), the Single Cell Analysis Core also provides state-of-the-art computational tools for identifying cellular subpopulations, differential expression, data visualization, and statistical analysis. Please contact to learn more and schedule a consult with our experts.

Standard Packages and Pricing*

10x Genomics Chromium 3' Solution microfluidic cell processing, library preparation, and sequencing (~5,000 cells): $3,343

Pooled 3'-End scRNA-Seq in 96-well plates, library preparation, and sequencing (~96 cells per plate): $766

96-well plate with reagents for Pooled 3'-End scRNA-Seq (for users to test or bank samples; library preparation and sequencing not included): $95

* Current prices are for Columbia users, are subsidized by institutional support, and subject to change. External users are welcome, but should request a quote.

Sample Submission

For experiments using 10x Genomics Chromium 3' Solution, researchers must coordinate the delivery of a dissociated suspension of live cells. For plate-based scRNA-Seq, researchers must submit 96-well plates containing the frozen lysates of individual cells sorted one at-a-time into each well. Researchers must use 96-well plates and reagents provided by the Core. All first-time users are required to schedule an in-person meeting to discuss projects with Peter Sims and Erin Bush ( Sample and billing information can be submitted using our web-based form.


The Single Cell Analysis Core gratefully acknowledges the following organizations for their generous support: