3 research outputs found
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
No full textWe present a major update of the HOCOMOCO collection that consists of patterns describing DNA binding specificities for human and mouse transcription factors. In this release, we profited from a nearly doubled volume of published in vivo experiments on transcription factor (TF) binding to expand the repertoire of binding models, replace low-quality models previously based on in vitro data only and cover more than a hundred TFs with previously unknown binding specificities. This was achieved by systematic motif discovery from more than five thousand ChIP-Seq experiments uniformly processed within the BioUML framework with several ChIP-Seq peak calling tools and aggregated in the GTRD database. HOCOMOCO v11 contains binding models for 453 mouse and 680 human transcription factors and includes 1302 mononucleotide and 576 dinucleotide position weight matrices, which describe primary binding preferences of each transcription factor and reliable alternative binding specificities. An interactive interface and bulk downloads are available on the web: http://hocomoco.autosome.ru and http://www.cbrc.kaust.edu.sa/hocomoco11. In this release, we complement HOCOMOCO by MoLoTool (Motif Location Toolbox, http://molotool.autosome.ru) that applies HOCOMOCO models for visualization of binding sites in short DNA sequences.The project was primarily supported by Russian Science Foundation [17-74-10188 to I.V.K.]; A.M.M. and V.B.B. were supported by King Abdullah University of Science and Technology (KAUST) [baseline fund BAS/1/1606-01-01 of V.B.B.]; I.E.V. was personally supported by the Skoltech Systems Biology Fellowship. Funding for open access charge: Russian Science Foundation [17–74–10188 to I.V.K.]
Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity
No full text(Cell Stem Cell 20, 518–532.e1–e9; April 6, 2017) In the originally published version of this manuscript, Caroline Hendry was inadvertently excluded from the author list. Her contributions to the work included the following: the development of SOPs for the relatively novel Sendai virus infection method for reprogramming; the design and implementation of studies to assess the variation among lines derived from a single donor (which included up to 14 lines per donor and analyses at both the iPSC stage and post-differentiation); and, together with S.L.D. and P.C., contributing to the development of an optimized workflow for the characterization of a large library of human iPSC lines, the creation and isolation of iPSCs, the performance of quality control for pluripotency markers, the serial passaging of each line for at least 12 passages, the verification that said lines were Sendai-free, the freezing down of cells at every split, the active maintenance of databases to catalogue the large number of lines and splits, and the preparation of these cells for RNA-seq analysis to be performed by members of the E.E.S. lab. All of these studies were performed to optimize the workflow that underpinned the project, and hence, the paper. All of the authors on the original author list, excluding those who are unable to be contacted and those who are deceased, have given their consent for Dr. Hendry's addition. The corrected author list is now included with this statement and the original manuscript online
