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Notes: The authors used the Roche 454 sequencing platform to perform a differential transcriptome analysis and identify genes that are differentially expressed in human buccal cancer and normal tissue. The quantity of first-strand and second-strand cDNA products was estimated using the QuantiFluor™-ST Fluorometer as well as the High Sensitivity DNA Chip kit and Agilent Bioanalyzer 2100. (4238)

Notes: These authors used the Roche 454 next generation sequencing platform to sequence and compare cancerous and normal horn tissue transcripts. mRNA isolated from each sample was fragmented prior to cDNA synthesis. cDNA quality was verified using a high sensitivity DNA Chip kit on the  Bioanalyzer 2100 and the  QuantiFluor™-ST Fluorometer. The transcripts were compared and potential tumor associated genes identified. (4229)

Notes: The authors studied the effect of butyrate treatment on histone acetylation and characterized how H3 acetylation affects DNA sequence binding specificity. To examine sequence specificity, they performed chromatin immunoprecipitation with butyrate-treated and untreated bovine kidney epithelial cells, quantified the recovered DNA, then sequenced the DNA by Illumina next-generation sequencing. DNA was quantitifed using the QuantiFluor™-ST Fluorometer. (4240)

Notes: The authors characterized the gut microbiota in two populations of Sprague Dawley rats—one that was fed the AIN93 diet and the other was fed the AIN93 diet with lowbush wild blueberry powder. After 6 weeks, rats were sacrificed and DNA was purified from the contents of the proximal colon and subjected to whole genome sequencing to identify the resident bacterial species. The DNA concentration was determined using the QuantiFluor™-ST Fluorometer prior to Illumina next-generation sequencing. (4239)

Notes: This paper describes a method for sequencing unknown viral isolates from tissue culture using anchored random reverse transcription and PCR, pyrosequencing and data analysis. RNA was extracted from tissue culture supernatants positive for viral antigens and used in RT-PCR with random primers. Amplification products were gel-purified and used in pyrosequencing reactions. A QuantiFluor™-P Fluorometer was used to measure copy number concentration relative to a standard, prior to Roche 454 pyrosequencing. (4231)

Notes: These authors performed metagenomic analysis to investigate any changes in composition of the microbial flora of the abomasa (ruminant 4th stomach compartment) in immune cattle after reinfection with the nematode Ostertagia ostertagi. DNA was extracted from abomasal contents using a QIAamp stool kit and the integrity verified using an Agilent Bioanalyzer 2000. PCR was then performed using primers targeting hypervariable regions of 16S rRNA genes. The amplified material was gel-purified and sequenced using the Roche 454 pyrosequencing system. DNA concentration was measured before and after PCR using the QuantiFluor™ Fluorometer.