gene family clustering was performed using OrthoMCL. For this analysis, we also used four other published firefly genomes, six selected coleopteran genomes, and the fruit fly genome as an outgroup (Supplementary Table7). A total of 17,166 orthologs were identified in these twelve species, 4727 ...
The promoter sequence of the bovine NPY gene was screened for the identification of different putative transcription factor binding sites (TFBS). In the 639 nt promoter region examined, a total of 61 TFBS bindings were predicted (core similarity >80% and matrix similarity >85%, both strands) ...
A novel xeno-free and feeder-cell-free system for human pluripotent stem cell culture. Protein Cell 3, 51–59 (2012). Article CAS PubMed PubMed Central Google Scholar Bergstrom, R., Strom, S., Holm, F., Feki, A. & Hovatta, O. Xeno-free culture of human pluripotent stem cells. ...
ARNold A web tool for the prediction of Rho-independent transcription terminators Rho-independent termination is a major mechanism of transcriptional arrest in bacteria that controls both normal 3 termination and a wide array of regulato... M Naville,A Ghuillot-Gaudeffroy,A Marchais,... - 《...
DNA affinity purification sequencing (DAP-seq) couples in vitro expression of transcription factor (TF) and binding to a genomic DNA library with next-generation sequencing, providing a robust method to identify genome-wide transcription factor binding sites (TFBS) on endogenous genomic DNA. Here we...
Conclusions We conclude that the LASAGNA algorithm is simple and effective in aligning variable-length binding sites. It has been integrated into a user-friendly webtool for TFBS search and visualization called LASAGNA-Search. The tool currently stores precomputed PSSM models for 189 TFs and 133 ...
Combining microarray expression profiling and ChIP-X data allows more effective TFBS analysis for studying the function of a TF. However, current web servers only provide tools to analyze either ChIP-X or expression data, but not both. Here, we present ChIP-Array, a web server that integrates...
For transactivation assay, the plasmid pGBKT7- BnaABF2 was made by inserting the cDNA fragment of BnaABF2 into the EcoRI/PstI cloning sites of vector pGBKT7 (Clontech). The sequences of primers used for plasmids constructions are listed in Additional file 1: Table S1. Agrobacterium ...
Binding of other TFs at SOX9 direct target sites substantially decreased RE sensitivity to SOX9 dosage; the strongest effects were seen for TWIST1 and TFAP2A, with minor effects of NR2F1 at TWIST1- and TFAP2A-bound REs (Fig. 3f). We replicated this result using TF sequence motifs (...
Cells were induced by plating in doxycycline-free growth medium, and samples were collected at time-points up to 72 h. (b) Glutaminase activity assay using mitochondria isolated from MEFs in which oncogenic-Dbl expression was either uninduced (+Dox) or induced for 24 h (−Dox). ...