Archives

  • 2018-07
  • 2018-10
  • 2018-11
  • 2019-04
  • 2019-05
  • 2019-06
  • 2019-07
  • 2019-08
  • 2019-09
  • 2019-10
  • 2019-11
  • 2019-12
  • 2020-01
  • 2020-02
  • 2020-03
  • 2020-04
  • 2020-05
  • br Specifications table br Value of

    2018-10-25


    Specifications table
    Value of the data
    Experimental design, materials and methods HEK293 cell lines expressing either hAha1–Y223F–FLAG or Y223E–FLAG were grown in Dulbecco׳s modified Eagle׳s minimal essential medium (DMEM, Invitrogen) supplemented with 10% fetal bovine serum [1–4]. All cell lines were propagated at 37°C in an atmosphere containing 5% CO2. Protein extraction from both HEK293 cells was carried out using methods previously described [5]. For immunoprecipitation, mammalian cell lysates were incubated with anti-FLAG antibody conjugated magnetic beads (Sigma) for 2h at 4°C and washed 4 times with fresh lysis buffer (20mM Tris (pH 7.5), 100mM NaCl, 1mM MgCl2, 0.1% NP40, Protease and Phosphatase inhibitor mini tablet, EDTA-free (Pierce). hAha1 complexes were eluted with FLAG peptide (Apex Bio).
    LC–MS/MS data acquisition
    Data The nucleic SCR7 cost sequence of the DNA control, J1 and each hybrid PNA–DNA junction is displayed in Fig. 1[1]. The data in Figs. 2–4 display the electrophoretic mobility patterns of six hybrid PNA–DNA 4WJs vs. i) J1 and ii) different combinations of potentially contaminating strands of DNA. The contaminating strands are composed of single strands used to form J1. The data are based on the protocol used by Kallenbach and Seaman to characterize, J1 [2,3]. In our previous study, each hybrid PNA–DNA 4WJ is evaluated vs. J1 [4].
    Experimental design, materials and methods
    Data interpretation The data provide a direct method to compare the mobility of immobile hybrid PNA–DNA junctions vs. a DNA control junction (J1) and potentially contaminating multi-PNAs. In each gel (Figs. 2–4); the single strand control (101) is loaded in lane 1, the contaminating strands are loaded in lanes 2–11, the DNA control, J1 is loaded in lane 12, and the hybrid PNA–DNA junctions are loaded in lanes 13 and 14. In each case, the hybrid 4WJ with a DNA overhang(s) is loaded in lane 13 and the blunt-ended construct is loaded in lane 14.
    Acknowledgments This work was supported by the Mississippi INBRE, funded by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM103476.
    Specifications
    Direct link to deposited data https://www.encodeproject.org http://www.mouseencode.org http://www.ncbi.nlm.nih.gov.eleen.top/geo/query/acc.cgi?acc=GSE44255 http://www.ncbi.nlm.nih.gov.eleen.top/geo/query/acc.cgi?acc=GSE59779 Individual dataset descriptions can be found in Table 1.
    Value of the data
    Data, experimental design, materials and methods Random inactivation of one of the X chromosomes in mammalian females takes place during early development and is associated with Xist coating, accumulation of repressive histone modifications and a specific alteration of chromatin architecture. A few genes escape random X inactivation and remain bi-allelicly expressed throughout the life of the organism. This data is associated with the research article focused on identifying escape genes in multiple tissue types in vivo, and on investigating a mechanism that contributes to expression from the inactive X using a novel hybrid mouse model.
    Acknowledgments We thank D. K. Nguyen (University of Washington) for helpful discussions and critical reading of the manuscript. We thank T. Sado (Kyushu University) for the Xist mutant mice. We are grateful to C. Lee (University of Washington) for his help with next-generation sequencing. This work is supported by grants GM046883 (JBB, XD, FY, CMD), GM098039 (WSN, WM), MH083949 (XD, CMD) and MH099628 (JBB, CMD) from the National Institutes of Health (NIH.gov). XD is also supported by a Junior Faculty Pilot award from the Department of Pathology at the University of Washington.
    Data C1q tumor necrosis factor α-related protein isoform 5 (CTRP5), a member of the CTRP family, has recently been identified as a highly conserved family of adiponectin paralog [2]. Adiponectin is an abundant adipokine involved in the regulation of energy metabolism, such as fatty acid oxidation and glucose utilization [3]. Similar to adiponectin, we have previously shown that the globular domain of CTRP5 (gCTRP5) activates AMPK, which subsequently stimulates fatty acid oxidation and glucose uptake in myocytes [4].