RNAseq expression analysis of the dental microbiome in twin pairs with and without dental Caries.
SUMMARY: The study aims to assess gene expression in plaque samples collected from twin pairs that are both concordant and discordant with respect to dental Caries diagnosis.
STUDY DESIGN: RNA was extracted from RNAprotect (Qiagen, In c.) treated dental plaque scrapings from 38 patients. Amplified cDNA was created and rRNA sequence was removed by subtractive hybridization. Individual patient samples were run on a single lane of an Illumina Genome Analyzer.
File Types consist of Illumina RNAseq data in FASTQ format. File Naming Conventions are as follows:
Patient ID : 4 digit identifier
Diagnosis : Caries Negative(CN) or Caries Positive(CP)
Type of Twin: Monozygotic(MZ)or Dizygotic(DZ)
Pair to xxxx: 4 digit twin identifier maps to the Patient ID
E.g: 2126_CP_MZ_PairTo_2125_fastqc - 2126 is a caries positive patient and pairs to monozygotic twin pair 2125.
CONTRIBUTORS: Ana C. Ong, Erik Snesrud, Jia Liu, Vasily A. Sharov, Walter A. Bretz and Scott N. Peterson
RNA-Seq Enrichment Protocol