GSE69471
Combined ultra-low input mRNA and whole-genome sequencing from human embryonic stem cells
Next Generation Sequencing has proven to be an exceptionally powerful tool in the field of genomics and transcriptomics. With recent development it is nowadays possible to analyze ultra-low input sample material down to single cells. Nevertheless investigating such sample material still limits the analysis to either the genome or transcriptome, hence a combined analysis of both types of nucleic acids from the same sample material is still in demand.We developed a protocol which enables the combined analysis of the genome as well as the transcriptome by Next Generation Sequencing from ultra-low input samples. The protocol was evaluated by sequencing sub-colony structures from human embryonic stem cells containing 150 to 200 cells. The method can be adapted to any available sequencing system (e.g. Illumina, SOLiD, 454, etc.).To our knowledge, this is the first report where sub-colonies of human embryonic stem cells have been analyzed both at the genomic as well as transcriptome level. The method of this proof of concept study may find useful practical applications for cases where only a limited number of cells are available, e.g. for tissues samples from biopsies, circulating tumor cells and cells from early embryonic development. The results we present demonstrate that a combined analysis of genomic DNA and messenger RNA from ultra low input samples is feasible and can readily be applied to other cellular systems with limited material available. Overall design: sequencing analysis of ultra-low amounts of RNA (in duplicate) and DNA from the same sample