Open Access Highly Accessed Methodology article

Single cell transcriptomic analysis of prostate cancer cells

Christopher J Welty1, Ilsa Coleman2, Roger Coleman2, Bryce Lakely1, Jing Xia2, Shu Chen2, Roman Gulati2, Sandy R Larson1, Paul H Lange13, Bruce Montgomery4, Peter S Nelson24, Robert L Vessella13 and Colm Morrissey15*

Author Affiliations

1 Department of Urology, University of Washington, Seattle, WA, USA

2 Fred Hutchinson Cancer Research Center, Seattle, WA, USA

3 Department of Veterans Affairs Medical Center, Seattle, WA, USA

4 Department of Medicine, University of Washington, Seattle, WA, USA

5 Genitourinary Cancer Research Laboratory, Department of Urology, University of Washington, Box 356510, Seattle, WA, 98195, USA

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BMC Molecular Biology 2013, 14:6  doi:10.1186/1471-2199-14-6

Published: 16 February 2013

Additional files

Additional file 1: Table S1:

Primer sequences, amplicon length, possible splice variants, 3’ bias, and primer specificity of the 10 genes examined by RT-qPCR in this study.

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Additional file 2: Table S2:

Quantitative RT-PCR of 4 housekeeping genes (ACTB, GAPDH, YWHAZ, and GAPDH) for each of the 10 single-, 5-, and 10-cell samples. * Indicates removed from analysis based on quality control. NTC = No template control; na = no amplification detected after 46 cycles; 10 pg and 100 pg represents C4-2B total RNA from the same original culture.

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Additional file 3: Table S3:

M ratio pair-wise correlation analysis for one cell. Based on the Dixon test for the correlation coefficients, the p-value for testing outliers is 0.457. Using p-value = 0.05 as cut-off. Array data: The microarray data for these experiments have been deposited in the Gene Expression Omnibus database (available at http://www.ncbi.nlm.nih.gov/geo webcite) under accession number GSE38416.

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Additional file 4: Table S4:

Gene Set Enrichment Analysis (GSEA) of single-, 5-, and 10-cell samples. GO = Gene Ontology; NES = Normalized Enrichment Score. The enrichment score reflects the degree to which the gene set is overrepresented at the extremes of the entire ranked list (n = 925).

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