Results 71 to 80 of about 596,095 (346)

Genome-Scale Validation of Deep-Sequencing Libraries

PLoS ONE, 2008
Chromatin immunoprecipitation followed by high-throughput (HTP) sequencing (ChIP-seq) is a powerful tool to establish protein-DNA interactions genome-wide. The primary limitation of its broad application at present is the often-limited access to sequencers.
D. Schmidt†, R. Stark†, M. D. Wilson, G. D. Brown, D. T. Odom.   +4 more
openaire   +5 more sources

Combined spatially resolved metabolomics and spatial transcriptomics reveal the mechanism of RACK1‐mediated fatty acid synthesis

Molecular Oncology, EarlyView.
The authors analyzed the spatial distributions of gene and metabolite profiles in cervical cancer through spatial transcriptomic and spatially resolved metabolomic techniques. Pivotal genes and metabolites within these cases were then identified and validated.
Lixiu Xu, Jinqiu Li, Junqi Ma, Ayshamgul Hasim   +3 more
wiley   +1 more source

Generating site saturation mutagenesis libraries and transferring them to broad host range plasmids using type IIS restriction enzymes [PDF]

arXiv, 2023
Protein engineering is an established method for tailoring enzymatic reactivity. A commonly used method is directed evolution, where the mutagenesis and natural selection process is mimicked and accelerated in the laboratory. Here, we describe a reliable method for generating saturation mutagenesis libraries by golden gate cloning in a broad host range
arxiv  

Cosmid Cloning of Five \u3cem\u3eZymomonas trp\u3c/em\u3e Genes by Complementation of \u3cem\u3eEscherichia coli\u3c/em\u3e and \u3cem\u3ePseudomonas putida trp\u3c/em\u3e Mutants [PDF]

, 1988
A library of Zymomonas mobilis genomic DNA was constructed in the broad-host-range cosmid pLAFR1. The library was mobilized into a variety of Escherichia coli and Pseudomonas putida trp mutants by using the helper plasmid pRK2013. Five Z.
Eddy, Christina Kay, Noel, K. Dale, Smith, Oliver H.   +2 more
core   +1 more source

Optimizing a PCR protocol for cpn60-based microbiome profiling of samples variously contaminated with host genomic DNA. [PDF]

, 2015
The current recommended protocol for chaperonin-60 (cpn60) universal target based microbiome profiling includes universal PCR of microbiome samples across an annealing temperature gradient to maximize the diversity of sequences amplified.
Chaban, B, Harding, JC, Hill, JE, Johnson, LA   +3 more
core   +1 more source

A Human Genomic Library Enriched in Transcriptionally Active Sequences (aDNA Library) [PDF]

Genome Research, 2000
Core histone hyperacetylation, in particular of H4, is concentrated in the promoter–upstream regions of active genes and in certain cases is locuswide. Antibodies to hyperacetylated H4 were used to immunoprecipitate dinucleosomal chromatin derived from K562 human erythroleukemic cells by micrococcal nuclease digestion. The extracted DNA was made into a
Pelling, A., Thorne, Alan, Crane-Robinson, Colyn   +2 more
openaire   +4 more sources

Circulating tumor DNA (ctDNA) trajectories predict survival in trifluridine/tipiracil‐treated metastatic colorectal cancer patients

Molecular Oncology, EarlyView.
The authors applied joint/mixed models that predict mortality of trifluridine/tipiracil‐treated metastatic colorectal cancer patients based on circulating tumor DNA (ctDNA) trajectories. Patients at high risk of death could be spared aggressive therapy with the prospect of a higher quality of life in their remaining lifetime, whereas patients with a ...
Matthias Unseld, Stefan Kühberger, Ricarda Graf, Christine Beichler, Markus Braun, Nadia Dandachi, Ellen Heitzer, Gerald W. Prager   +7 more
wiley   +1 more source

Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. [PDF]

, 2012
BAckground: Massively parallel sequencing technology is revolutionizing approaches to genomic and genetic research. Since its advent, the scale and efficiency of Next-Generation Sequencing (NGS) has rapidly improved. In spite of this success, sequencing
Campino, Susana, Gu, Yong, Kwiatkowski, Dominic P, Macinnis, Bronwyn, Manske, Magnus, Maslen, Gareth, Otto, Thomas D, Oyola, Samuel O, Quail, Michael A, Swerdlow, Harold P, Turner, Daniel J   +10 more
core  

Crosstalk between gut microbiota and tumor: tumors could cause gut dysbiosis and metabolic imbalance

Molecular Oncology, EarlyView.
In this research, we analyzed the relationship between gut microbiota and tumor. We discovered that both subcutaneous and metastatic tumors would alter the composition and metabolic function of gut microbiota. Meanwhile, fecal microbiota transplantation also indicated the anti‐tumor role of the gut microbiota, revealing the crosstalk between tumor and ...
Siyuan Zhang, Haimei Wen, Ying Chen, Jingya Ning, Di Hu, Yujiao Dong, Chenyu Yao, Bo Yuan, Shuanying Yang   +8 more
wiley   +1 more source

Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea

mBio
The identification of microbial genes essential for survival as those with lethal knockout phenotype (LKP) is a common strategy for functional interrogation of genomes.
Kira S. Makarova, Changyi Zhang, Yuri I. Wolf, Svetlana Karamycheva, Rachel J. Whitaker, Eugene V. Koonin   +5 more
doaj   +1 more source