mRNA-sequencing whole transcriptome analysis of a single cell on the SOLiD system

• Published in: Journal of biomolecular techniques Vol. 20; no. 5; pp. 266 - 271
• Main Authors: Lao, Kai Q, Tang, Fuchou, Barbacioru, Catalin, Wang, Yangzhou, Nordman, Ellen, Lee, Clarence, Xu, Nanlan, Wang, Xiaohui, Tuch, Brain, Bodeau, John, Siddiqui, Asim, Surani, M Azim
• Format: Journal Article
• Language: English
• Published: United States Association of Biomolecular Resource Facilities 01.12.2009
• Subjects: ABRF 2009 Selected Presentations; Animals; Chromosome Mapping; DNA, Complementary - metabolism; Gene Expression Profiling; Gene Expression Regulation, Developmental; Genetic Techniques; Mice; Mice, Knockout; Oligonucleotide Array Sequence Analysis - methods; Oocytes - metabolism; RNA, Messenger - metabolism; Sequence Alignment; Sequence Analysis, RNA - methods; Dicer; Ago2; gene expression
• ISSN: 1524-0215; 1943-4731

We have developed a sequencing-based gene expression profiling assay at single-cell resolution by combining a modified single-cell whole transcriptome amplification method with the next generation sequencing technique, the SOLiD system. Using this assay, we have shown that blastomeres in a four-cell stage embryo have similar gene expression, which is compatible with the fact that they have similar developmental potential. We proved that compared with cDNA microarray technique, our single-cell cDNA SOLiD sequencing assay can detect expression of thousands of more genes. Moreover, for the genes detected by microarray and SOLiD sequencing, our assay detected new transcript variants for a large proportion of them, which confirms unambiguously at single-cell resolution that the transcriptome complexity is higher than expected traditionally. Finally, by using our assay to Dicer knockout (KO) and Ago2 KO oocytes, we showed that a significant amount of transposons were up-regulated abnormally in Dicer/Ago2 KO mature oocytes compared with wild-type controls.