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Series GSE125085 Query DataSets for GSE125085
Status Public on Jan 16, 2019
Title Method for absolute quantification of microbial communities by using both microarrays and competitive PCR
Platform organisms Bacteria; Treponema denticola; Campylobacter rectus; Aggregatibacter actinomycetemcomitans; Porphyromonas gingivalis; Capnocytophaga gingivalis; Streptococcus gordonii; Streptococcus mutans; Streptococcus intermedius; Tannerella forsythia; Prevotella intermedia; Fusobacterium nucleatum subsp. nucleatum
Sample organisms Treponema denticola; Campylobacter rectus; Helicobacter pylori; Pseudomonas aeruginosa; Acinetobacter baumannii; Neisseria meningitidis; Escherichia coli; Aggregatibacter actinomycetemcomitans; Phocaeicola vulgatus; Porphyromonas gingivalis; Fusobacterium nucleatum; Capnocytophaga gingivalis; Cereibacter sphaeroides; Staphylococcus aureus; Staphylococcus epidermidis; Deinococcus radiodurans; Streptococcus gordonii; Streptococcus mutans; Streptococcus agalactiae; Streptococcus intermedius; Enterococcus faecalis; Bacillus cereus; Clostridium beijerinckii; Lactobacillus gasseri; Schaalia odontolytica; Bifidobacterium adolescentis; Cutibacterium acnes; Homo sapiens; Tannerella forsythia; Prevotella intermedia; Prevotella nigrescens
Experiment type Other
Summary We investigated an improved method that combines competitive PCR and microarray techniques. This approach allowed us to quantify specific bacterial groups mounted on DNA chips with accuracy close to that of real-time PCR, despite a measurement at the end point of PCR, and also to estimate the bacterial DNA content in sample DNA.
 
Overall design Two bacterial genomic DNA mixtures for calibration curve, twelve kinds of bacterial genomic DNA (4 dilution series, duplicate) for specificity test of DNA chip probes were used.
One bacterial genomic DNA mixture and extraction DNA samples from five human dental plaque samples with a sterile toothbrush (triplicate) were measured.
Web link https://www.sciencedirect.com/science/article/pii/S0167701219304178
 
Contributor(s) Hoashi N, Togawa N, Yazawa A
Citation(s) 31513858
Submission date Jan 15, 2019
Last update date Sep 13, 2019
Contact name Naoyuki Togawa
E-mail(s) togawa.naoyuki.ms@m-chemical.co.jp
Phone +81-45-504-1139
Organization name Mitsubishi Chemical Corporation
Lab Tsurumi R&D Center
Street address 10-1,Daikokucho,Tsurumi-ku
City Yokohama
State/province Kanagawa
ZIP/Postal code 230-0053
Country Japan
 
Platforms (1)
GPL25612 DNAchip_Genopal_ORAL_ver.1
Samples (178)
GSM3562404 8 kinds of bacterial genomic DNA mixture_dilution_step0_n=1
GSM3562405 8 kinds of bacterial genomic DNA mixture_dilution_step0_n=2
GSM3562406 8 kinds of bacterial genomic DNA mixture_dilution_step0_n=3
Relations
BioProject PRJNA515193

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE125085_RAW.tar 760.0 Kb (http)(custom) TAR (of CSV)
Processed data included within Sample table
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