Populations of very small embryonic-like stem cells (VSELs) (CD34+lin-CD45- and CD133+lin-CD45-), circulating in the peripheral blood of adults in small numbers, have been identified in several human tissues and together with the populations of hematopoietic stem cells (HSCs) (CD34+lin-CD45+) and CD133+lin-CD45+constitute a pool of cells with self-renewal and pluripotent stem cell characteristics. Using advanced cell staining and sorting strategies, we isolated populations of VSELs and HSCs for bulk RNA-Seq analysis to compare the transcriptomic profiles of both cell populations. Libraries were prepared from an extremely small number of cells; however, their good quality was preserved, and they met the criteria for sequencing. We present here a step-by-step NGS protocol for sequencing VSELs and HSC with a description of troubleshooting during library preparation and sequencing.
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