human oral metagenome
collection_date
2014
description
apical root canal system of teeth with post-treatment apical periodontitis
env_biome
human-associated habitat
env_feature
tooth
env_material
root canal system of teeth
geo_loc_name
Brazil
host
Homo sapiens
host_age
38
host_sex
female
lat_lon
23.01 S 43.44 W
organism
human oral metagenome
sample_title
sample 42
seq_methods
"The 16S rRNA gene V4 variable region PCR primers 515/806 (CAPORASO et al., 2011) with barcode on the forward primer were used in a 30 cycle PCR (5 cycle used on PCR products) using the HotStarTaq Plus Master Mix Kit (Qiagen, USA) under the following conditions: 94oC for 3 minutes, followed by 28 cycles of 94oC for 30 seconds, 53oC for 40 seconds and 72oC for 1 minute, after which a final elongation step at 72oC for 5 minutes was performed. After amplification, PCR products are checked in 2% agarose gel to determine the success of amplification and the relative intensity of bands. Multiple samples are pooled together in equal proportions based on their molecular weight and DNA concentrations. Pooled samples are purified using calibrated Ampure XP beads. Then the pooled and purified PCR product is used to prepare DNA library by following Illumina TruSeq DNA library preparation protocol. Paired-end sequencing was performed at MR DNA (www.mrdnalab.com, Shallowater, TX, USA) on a MiSeq following the manufacturer's guidelines. The sequences from each end were joined after quality q25 trimming of the ends with MR DNA pipeline. "
BioSampleModel
MIMARKS.survey
BioSampleModel
MIGS/MIMS/MIMARKS.human-oral