title: qiime_experiment_820:639906:1
design: The extracted DNA was not pooled, and each sample represents the DNA from the biofilm of single kelp individual. DNA was eluted with 30 ul water and samples were diluted accordingly to a final concentration of 20 ng/L. DNA samples were quantified using a Nanodrop spectrophotometer (Nyxor Biotech, Paris, France).
library_construction_protocol: Multiplexed bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) was performed using the Titanium platform (Roche Applied Science, Indianapolis, IN) as previously described (Dowd et al. 2008) in a commercial facility (Research and Testing Laboratories, Lubbock, TX). Briefly, a single step PCR using the primers that span the variable regions V1???V3 of the 16S gene, 28F 5??_GAGTTTGATCNTGGCTCAG and 519r 5??_GTNTTACNGCGGCKGCTG), was used to amplify the 16S rRNA genes as well as to introduce adaptor sequences and sample-specific 8-mer oligonucleotide tags (barcodes) into the DNA. The same bar codes were utilized for each primer set. The initial generation of the sequencing library used a one-step polymerase chain reaction (PCR) with a total of 30 cycles, a mixture of HotStart and HotStar high fidelity taq polymerases (Qiagen).
attributes.tag: experiment_title
attributes.value: Kelp associated bacteria
attributes.tag: key_seq
attributes.value: TCAG
attributes.tag: sample_center
attributes.value: MBRI
attributes.tag: sequencing_meth
attributes.value: pyrosequencing
attributes.tag: run_date
attributes.value: 6/7/10
attributes.tag: experiment_center
attributes.value: MBRI
attributes.tag: pcr_primers
attributes.value: FWD:GAGTTTGATCNTGGCTCAG; REV:GTNTTACNGCGGCKGCTG
attributes.tag: region
attributes.value: 2
attributes.tag: run_center
attributes.value: MBRI
attributes.tag: target_subfragment
attributes.value: V13
attributes.tag: platform
attributes.value: Titanium
attributes.tag: library_construction_protocol
attributes.value: Multiplexed bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) was performed using the Titanium platform (Roche Applied Science, Indianapolis, IN) as previously described (Dowd et al. 2008) in a commercial facility (Research and Testing Laboratories, Lubbock, TX). Briefly, a single step PCR using the primers that span the variable regions V1???V3 of the 16S gene, 28F 5??_GAGTTTGATCNTGGCTCAG and 519r 5??_GTNTTACNGCGGCKGCTG), was used to amplify the 16S rRNA genes as well as to introduce adaptor sequences and sample-specific 8-mer oligonucleotide tags (barcodes) into the DNA. The same bar codes were utilized for each primer set. The initial generation of the sequencing library used a one-step polymerase chain reaction (PCR) with a total of 30 cycles, a mixture of HotStart and HotStar high fidelity taq polymerases (Qiagen).
attributes.tag: experiment_design_description
attributes.value: The extracted DNA was not pooled, and each sample represents the DNA from the biofilm of single kelp individual. DNA was eluted with 30 ul water and samples were diluted accordingly to a final concentration of 20 ng/L. DNA samples were quantified using a Nanodrop spectrophotometer (Nyxor Biotech, Paris, France).
attributes.tag: row_number
attributes.value: 1
attributes.tag: target_gene
attributes.value: 16S rRNA
attributes.tag: study_center
attributes.value: Stanford University