Embodiments of the disclosure include systems, methods, and compositions for producing megakaryocytes and platelets for recipient individuals in need thereof. The megakaryocytes and platelets are produced following co-culture of MSCs and CD34+ cells in media comprising stem cell factor, thrombopoietin, and IL-6, and wherein at least the CD34+ cells have a knock-in of HLA-E at the beta-2-microglobulin genomic locus, in specific embodiments. In some cases, ROCK inhibitors are utilized.

The invention provides compositions and methods for manufacturing pluripotent cells. In particular, the invention provides improved culture platforms for manufacturing pluripotent cells with ground state pluripotency. In various embodiments, the invention contemplates, in part, a composition comprising: (a) a Wnt pathway agonist; (b) a MEK inhibitor; and (c) a ROCK inhibitor. In certain embodiments, the composition further comprises bFGF or LIF.

The present invention provides for methods of epigenetic analysis. In some cases, the methods may include obtaining a sample comprising a nucleic acid sequence. In some cases, the nucleic acid sequence may comprise one or more epigenetic marks. The methods may include performing a sequencing. The methods may include distinguishing a hydroxymethylated base from a methylated base.

The invention provides compositions and methods for manufacturing pluripotent cells. In particular, the invention provides improved culture platforms for manufacturing pluripotent cells with ground state pluripotency. In various embodiments, the invention contemplates, in part, a composition comprising: (a) a Wnt pathway agonist; (b) a MEK inhibitor; and (c) a ROCK inhibitor. In certain embodiments, the composition further comprises bFGF or LIF.

Provided herein are methods and compositions for inducing chemical senescence in neurons and methods of using chemically induced senescent neurons for modeling neurodegenerative disease and drug discovery. The methods include contacting human neurons with a culture medium comprising an inhibitor of DNA glycosylase 1, an autophagy inhibitor, and an HIV protease inhibitor to obtain an in vitro population of senescent neurons within about 4 days. When the neurons are obtained from a patient having a neurodegenerative disease, chemically induced senescent neurons obtained by these methods recapitulate cellular and subcellular phenotypes observed in individuals with the neurodegenerative disease.

The present invention provides for novel methods for regulating and detecting the cytosine methylation status of DNA. The invention is based upon identification of a novel and surprising catalytic activity for the family of TET proteins, namely TET1, TET2, TET3, and CXXC4. The novel activity is related to the enzymes being capable of converting the cytosine nucleotide 5-methylcytosine into 5-hydroxymethylcytosine by hydroxylation.

The present invention provides for methods of epigenetic analysis. In some cases, the methods may include obtaining a sample comprising a nucleic acid sequence. In some cases, the nucleic acid sequence may comprise one or more epigenetic marks. The methods may include performing a sequencing. The methods may include distinguishing a hydroxymethylated base from a methylated base.

The present invention provides for methods of epigenetic analysis. In some cases, the methods may include obtaining a sample comprising a nucleic acid sequence. In some cases, the nucleic acid sequence may comprise one or more epigenetic marks. The methods may include performing a sequencing. The methods may include distinguishing a hydroxymethylated base from a methylated base.

Compositions are provided compositions comprising tankyrase/PARP (poly-ADP-ribose polymerase, also known as poly-ADP-ribosyltransferase) inhibitor-regulated naïve human induced pluripotent stem cells (N-hiPSCs) and their use in the treatment of vascular disorders.

Disclosed are methods and products for improving the quality of sperm, methods for treating subjects to improve sperm quality or improve fertility, and use of sperm with improved quality in assisted reproductive technologies, including exposing the sperm to BGP-15 and/or a derivative thereof, such as BGP-15, propanolol, bimoclomol, arimoclomal, NG94, iroxanadine, and/or a pharmaceutically acceptable derivative, prodrug, solvate, salt, tautomer, stereoisomer, and/or racemate thereof.