Comprehensive 16S rRNA Gene Sequencing of CP Samples

As per [10 (link)], (a) amplification of full length 16S ribosomal gene (1464 bp) from 50 ng/μl DNA from each CP sample using V1-V9 variable region primers; (b) barcoding of each amplified amplicon using paired 16-nt symmetric barcodes (https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Barcoding-with-SMRT Analysis-2.3) (Table 1); (c) multiplexing of barcoded-purified amplicons in a group of 5 libraries (Supplementary Table 2); and (d) Sequencing using DNA Sequencing Reagent Kit 4.0 v2 (Pacific Biosciences, USA) in a total of 24 SMRT cells (3 cells/library) using 6-hour movies data collection protocol were performed.

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Chowdhry R., Singh N., Sahu D.K., Tripathi R.K., Mishra A., Singh A., Mukerjee I., Lal N., Bhatt M.L, & Kant R. (2019). Dysbiosis and Variation in Predicted Functions of the Granulation Tissue Microbiome in HPV Positive and Negative Severe Chronic Periodontitis. BioMed Research International, 2019, 8163591.

Publication 2019

DNA Sequencing Reagent Kit 4.0 v2

Cells Gene amplification Library Primers Ribosomal Smrt

Corresponding Organization : King George's Medical University

Other organizations : All India Institute of Medical Sciences Rishikesh

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Variable analysis

independent variables

Amplification of full length 16S ribosomal gene (1464 bp) from 50 ng/μl DNA from each CP sample using V1-V9 variable region primers
Barcoding of each amplified amplicon using paired 16-nt symmetric barcodes
Multiplexing of barcoded-purified amplicons in a group of 5 libraries
Sequencing using DNA Sequencing Reagent Kit 4.0 v2 (Pacific Biosciences, USA) in a total of 24 SMRT cells (3 cells/library) using 6-hour movies data collection protocol

dependent variables

Not explicitly mentioned

control variables

Not explicitly mentioned

controls

Positive control: Not specified
Negative control: Not specified

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