Comprehensive qPCR profiling of gene expression in single neuronal cells

Ami Citri*, Zhiping P. Pang, Thomas C. Südhof, Marius Wernig, Robert C. Malenka

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

129 Scopus citations


A major challenge in neuronal stem cell biology lies in characterization of lineage-specific reprogrammed human neuronal cells, a process that necessitates the use of an assay sensitive to the single-cell level. Ssingle-cell gene profiling can provide definitive evidence regarding the conversion of one cell type into another at a high level of resolution. The protocol we describe uses Fluidigm Biomark dynamic arrays for high-throughput expression profiling from single neuronal cells, assaying up to 96 independent samples with up to 96 quantitative PCRpcr (qPCRpcr) probes (equivalent to 9,216 reactions) in a single experiment, which can be completed within 2-3 d. protocol enables simple and cost-effective profiling of several hundred transcripts from a single cell, and it could have numerous utilities.

Original languageAmerican English
Pages (from-to)118-127
Number of pages10
JournalNature Protocols
Issue number1
StatePublished - Jan 2012
Externally publishedYes

Bibliographical note

Funding Information:
acknowleDGMents A.C. acknowledges the generous support of the AXA Research Fund. Z.P.P. is supported by the Brain and Behavior Research Foundation (National Alliance for Research on Schizophrenia and Depression (NARSAD) Young Investigator Award) and the Robert Wood Johnson Foundation. We thank N. Yang for help in experimental work. We thank S. Chavez for initial instruction in the use of the Fluidigm Biomark system, and R. Reijo Pera for access to the Fluidigm Biomark system in her lab. We also thank members of the Malenka and Südhof labs for their comments on the manuscript.


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