Examining RNA Transcript Changes in Stem Cells Undergoing Differentiation, Using Short and Long Reads Sequencing Technologies [Nanopore long reads]

We explored changes at gene-level or transcript-level in embryonic stem cells, before and after in vitro differentiation with retinoic acid. RNA was sequenced both via Illumina short reads, and with Oxford Nanopore Technology with cDNA and direct RNA sequencing. Mouse embryonic stem cells were grown for 4 days in mES growth medium (DMEM, 15% FBS, L-Glutamine, Non-Essential Amino Acids) were harvested and named sample "undiff". Cells after additional treatmeant for 4 days with 2microM Retinoic Acid were harvested and named "day4". RNA was extracted and prepared for Illumina TruSeq Strand Specific sequencing, and to nanopore cDNA and direct RNA sequencing.