Project description:Iron-rich pelagic aggregates (iron snow) were collected directly onto silicate glass filters using an electronic water pump installed below the redoxcline. RNA was extracted and library preparation was done using the NEBNext Ultra II directional RNA library prep kit for Illumina. Data was demultiplied by GATC sequencing company and adaptor was trimmed by Trimgalore. After trimming, data was processed quality control by sickle and mRNA/rRNA sequences were sorted by SortmeRNA. mRNA sequences were blast against NCBI-non redundant protein database and the outputs were meganized in MEGAN to do functional analysis. rRNA sequences were further sorted against bacterial/archeal 16S rRNA, eukaryotic 18S rRNA and 10,000 rRNA sequences of bacterial 16S rRNA, eukaryotic 18S rRNA were subset to do taxonomy analysis.
Project description:Novel exhaled breath condensate device tests 4 times. Each test generated a single saliva sample and a corresponding exhaled breath condensate sample
Project description:An Easy Operating Pathogen Microarray (EOPM) was designed to detect almost all known pathogens and related species based on their genomic sequences. For effective identification of pathogens from EOPM data, a statistical enrichment algorithm has been proposed and further implemented in a user-friendly interface. A microarray was designed with probes for vertebrate-infecting virus sequences in EMBL, 18S rRNA fungi and parasite sequences from EMBL, and 16S rRNA sequences of bacteria from RDP, synthesized on the Agilent platform. The array was tested using 2 color dyes on cultured microbes and on clinical samples from sick and healthy people, looking for differences in clinically ill people compared to a number of healthy "controls".
Project description:Microbiome DNA from the adhering fraction of a sheep rumen. The RSTs were generated using an improved version of SARST (referred to as iSARST) from the microbiome DNA extracted from the adhering fraction of the rumen content taken from a sheep. The iSARST method is going to be submitted to Nature Biotechnology for publication. Keywords: other
Project description:Total DNA was extracted from stool specimens, amplified to collect amplicons of variable V3–V4 regions of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.
Project description:Investigation of the phylogenetic diversity of Acidobacteria taxa using PCR amplicons from positive control 16S rRNA templates and total genomic DNA extracted from soil and a soil clay fraction
Project description:Total DNA was extracted from saliva and stool of the patients, amplified to collect amplicons of variable V3–V4 regions of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.
Project description:We used phylogenetic low-density microarrays targeting the 16S rRNA gene to characterize the gingival flora of acute noma and acute necrotizing gingivitis lesions, and compared them to healthy control subjects of the same geographical and social background. Various types of samples were collected (column characteristics); patients from the same hospital without mouth infection (H), matched control populations (T), patients suffering gengivitis (Gengivitis), patient suffering NOMA (noma), patient suffering NOMA receiving antimicrobials (N-ATB). Sampled from patients were retrieved from both sides (column Description); healthy- or lesion-side of the mouth. All controls are matched with specific patients (see column patient category and number) We designed low-density 16S rDNA arrays representing 339 different phylotypes. We used an arbitrary cutoff of 1% of overall abundance to select from this dataset the most abundant sequences for probe design. Using this cutoff, the 132 most abundant 16S rRNA gene sequences were scanned for probes respecting defined physico-chemical properties (Tm = 65M-BM-15M-BM-0C; probe length = 23M-bM-^@M-^S50 nt; < -5.0 kcal/mol for hairpins; < -8.0 kcal/mol for self-dimers; and dinucleotide repeats shorter than 5 bp) using a commercial software (Array Designer TM 2.0 by Premier Biosoft). The 335 oligonucleotide probes were synthesized with a C6-linker with free primary amine (Sigma-Aldrich) and spotted on ArrayStrips microarrays (Clondiag GmbH, Jena, Germany).
