Resources by Category: "RNA-seq"

Genomic Characterization of Metformin Hepatic Response

Marcelo R. Luizon, Walter L. Eckalbar, Yao Wang, Stacy L. Jones, Robin, P. Smith, Megan Laurance5, Lawrence Lin1, Paul J. Gallins6, Amy S. Etheridge, Fred Wright, Yihui Zhou, Cliona Molony, Federico Innocenti, Sook Wah Yee, Kathleen, M. Giacomini, Nadav Ahituv. PLOS Genetics. Published: November 30, 2016.

FOXA1, GATA3 and PPARɣ Cooperate to Drive Luminal Subtype in Bladder Cancer: A Molecular Analysis of Established Human Cell Lines

Joshua I. Warrick, Vonn Walter, Hironobu Yamashita, Eunah Chung, Lauren Shuman, Vasty Osei Amponsa, Zongyu Zheng, Wilson Chan, Tiffany L. Whitcomb, Feng Yue, Tejaswi Iyyanki, Yuka I. Kawasawa, Matthew Kaag, Wansong Guo, Jay D. Raman, Joo-Seop Park & David J. DeGraff.  Scientific Reports 6, Article number: 38531 (2016). doi:10.1038/srep38531

Characterization of the cytokinin-responsive transcriptome in rice

  Tracy Raines, Ivory C. Blakley, Yu-Chang Tsai, Jennifer M. Worthen, José Manuel Franco Zorrilla, Roberto Solano, G. Eric Schaller, Ann E. Loraine and Joseph J. Kieber. BMC Plant Biology. 201616:260. DOI: 10.1186/s12870-016-0932-z  

Comparison of Sequencing Results of Commercially Available miRNA NGS Library Preparation Kits

M.J. Gonzalez-Plasky, A.M. McNulty, K. Charizanis, M. Carroll, E. Jan, K. Hecker, E. Kamberov miRNA sequencing (miRNA-Seq) is a useful tool for aiding researchers in the examination of miRNA expression patterns, the characterization of novel miRNAs, and for uncovering miRNA-disease associations. Since miRNAs are also unusually well-preserved in a range of specimens (e.g. urine, FFPE… Read more »

SCML2 establishes the male germline epigenome through regulation of histone H2A ubiquitination

“For both ChIP-seq and RNA-seq, the DNA libraries were prepared with NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (NEB) and Agencourt AMPure XP (Beckman Coulter) or ThruPLEX kit (Rubicon Genomics).”
Authors show that genes commonly expressed in somatic lineages and spermatogenesis-progenitors undergo repression in a genome-wide manner late in germline development. SCML2 works with PRC1 to promote ubiquitination of histone H2A on autosomes, repressing somatic/progenitor genes. SCML2 also prevents H2A ubiquitination on sex chromosomes during meiosis. This allows unique programming of sex chromosomes for male reproduction. Genomics work: RNA-seq of germlines showed that spermatocytes and spermatids showed different patterns of gene expression from embryonic cells, mitotic phase germline stem cells and THY1+ cells. ChIP-seq of SCML2 found it frequently localized to sites of PRC1 action (Hoxd and Htra1) and shared peaks with RNF2 and BMI1. *Click on title for publication details.*