The present invention relates to a bioreactor apparatus, and methods of use, for the isolation of rare blood cells, including hematopoietic stem cells and megakaryocytes. The apparatus includes a soft substrate and an anti-contractility agent, thereby providing a soft microenvironment to cultured cells. The apparatus of the invention is permissive for the survival of non-dividing cells while dividing cells are eliminated. This unique property allows for the simple isolation of rare blood cells without the use of costly equipment and antibodies.