Project description:We have used Agilent whole genome arrays (v4) to compare the gene expression changes between 10-day-old Arabidopsis wild type seedlings and arf2-8 (Ellis et al., 2005), gnc gnl (Richter et al., 2011) and arf2 gnc gnl mutants (all Col ecotype).
Project description:Total DNA was extracted from the stool of the patients, amplified to collect amplicons of variable V3–V4 regions (primers 341F and 805R) of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.
Project description:We examined 36 biopsies taken from digital dermatitis lesions of Holstein cows. The target was the V3 -V4 variable region of 16S rRNA using Treponema specific primers. We identified 20 different taxa of Treponema using this approach.
Project description:We report the use of high-throughput sequencing technology to detect the microbial composition and abundance of mice grastic contents before and after Helicobacter pylori infection or Lactobacillus paracasei ZFM54 pretreatment/treatment. The genomic DNA was obtained by the QIAamp PowerFecal DNA Kit. Then, the DNA samples were sent to BGI Genomics Co., Ltd. (Shenzhen, China) for V3-V4 region of the 16S rRNA gene high-throughput sequencing with an Illumina MiSeq platform. DNA samples were sequenced using primers 338F (forward primer sequence ACTCCTACGGGAGGCAGCAG)-806R (reverse primer sequence GGACTACHVGGGTWTCTAAT). The sequencing analyses were carried out using silva138/16s database as a reference for the assignation of Amplicon Sequence Variant (ASV) at 100% similarity.
Project description:We examined 36 biopsies taken from digital dermatitis lesions of Holstein cows. The target was the V3 -V4 variable region of 16S rRNA using Treponema specific primers. We identified 20 different taxa of Treponema using this approach. Phylogenetic study of the Treponema taxa found in digital dermatitis lesions of Holstein cows.
Project description:We report the use of high-throughput sequencing technology to detect the microbial composition and abundance of human feces after in vitro co-fermentation with citrus peel flavonoid extracts. The genomic DNA was obtained by the QIAamp PowerFecal DNA Kit. Then, the DNA samples were sent to Biomarker Bio-Tech (Beijing, China) for V3-V4 region of the 16S rDNA gene high-throughput sequencing with an Illumina MiSeq platform. DNA samples were sequenced using primers 338F (forward primer sequence ACTCCTACGGGAGGCAGCAG)-806R (reverse primer sequence GGACTACHVGGGTWTCTAAT). A total of 8,816,250 pairs of Reads were obtained from the 112 samples sequenced, and 8,721,112 Clean Reads were generated from the double-ended Reads after quality control and splicing. The sequencing analyses were carried out using the SILVA database as a reference for the assignation of operational taxonomic units (OTUs) with 97% of identity.
Project description:We have used Agilent whole genome arrays (v4) to compare the gene expression changes between 10-day-old Arabidopsis wild type seedlings and arf2-8 (Ellis et al., 2005), gnc gnl (Richter et al., 2011) and arf2 gnc gnl mutants (all Col ecotype). Three independent biological samples were prepared for each genotype.
Project description:The aim of this study was to use NGS RNAseq deep-sequencing in order to characterize the polyadenylated mRNAs and lncRNAs expressed in LNCaP cells treated with androgen hormone compared with untreated LNCaP cells (GSE79301). Trimmed reads were mapped using the hg19 genome with TopHat v.2.0.12 and Bowtie v.2.2.3. The assembly was guided by a custom GTF file created with transcripts fromhuman lncRNA annotations from GENCODE v19 (Harrow, Frankish et al.2012) and those already annotated as lincRNAs in (Cabili, Trapnell et al. 2011; Prensner, Iyer et al. 2011; Hangauer, Vaughn et al. 2013). The diferencial expression was calculated by the sum of exon read count per gene with HTSeq (Anders, Pyl et al. 2015), followed by a DESeq2 analysis (Love, Huber et al. 2014).
Project description:Maslinic acid is a novel phytochemical reported to exert prominent anti-cancer effects and it was hypothesized that this compound induces cellular apoptosis through the activation of the mitochondrial apoptotic pathway (Martin et al, 2007) — thereby resulting in significant inhibition of cell proliferation in a dose-dependent manner (Reyes-Zurita et al, 2009). Prior studies on maslinic acid in its function as a time-dependent inhibitor in both tumorigenesis and inflammation events by targeting multiple signaling pathways; particularly the NF-ĸB, MAPK (Li et al, 2010; Yap, et al, 2011) and JNK (Reyes-Zurita et al, 2011) pathways were mostly based on proteomic analyses (Li et al, 2010; Yap et. al., 2011). However, these results may not depict an accurate scenario of the signaling networks involved due to protein degradation, alternate splicing and extensive post-translational processing. Hence, this study aimed to construct a temporal-based global gene expression profile of the effects of maslinic acid by using the microarray technology. The aim of this project is to construct the complete global mRNA profile of the effects of maslinic acid in inhibiting early-antigen formation in Raji cells.