DOI: 10.57760/sciencedb.28999
title: 16S rRNA and Sequencing data of fecal samples
title: 16S rRNA and Sequencing data of fecal samples

description: Fecal samples of 31 individuals with hepatitis B virus (HBV)-infected liver cirrhosis before any therapeutic intervention (liver cirrhosis was determined by Hepatitis B, biopsy or two imaging methods (ultrasound, CT, and MRI) and 15 uninvolved healthy volunteers (without physical and psychological diseases from the people of a regular healthy physical examination every year by detecting the blood, urine and fecal routine, liver function, biochemical analysis, hepatitis markers, chest X-ray, abdominal ultrasound and so on) were acquired.Fecal sample collection was performed by using a TinyGene fecal collection box according to the manufacturer’s instructions (TinyGene, Shanghai), and the boxes were placed on ice as soon as possible and stored at -80℃ before further analysis.The 46 samples were subjected to library preparation (including genomic DNA extraction, PCR amplification, recovery using the AxyPrep DNA Gel Extraction Kit, and real-time fluorescence quantification on the FTC-3000TM real-time PCR instrument), followed by Illumina high-throughput sequencing and bioinformatics analysis.The 16S rRNA gene was amplified using primers 515F 5’-GTGCCAGCMGCCGCGGTAA-3’ and 926R 5’-CCGTCAATTCMTTTGAGTTT-3’ targeting the V5-V6 hyper-variable regions and sequenced in the Illumina platform following the manufacturer’s protocols. The sequencing data analysis was performed by using software of Trimmomatic, FLASH and Mothur V.1.39.5 according to the protocol. The Reads obtained by Illumina Miseq sequencing were distinguished according to the barcode, dereplicated and single Reads were discarded, and then filtered Reads were clustered into operational taxonomic units (OTU) assuming 97% similarity, and the optimized sequence was obtained finally. Each OTU was taxonomically assigned using Uclust considering a minimum percentage of similarity to a reference database (Silva 128 and Greengene) match of 90%.
description: Fecal samples of 31 individuals with hepatitis B virus (HBV)-infected liver cirrhosis before any therapeutic intervention (liver cirrhosis was determined by Hepatitis B, biopsy or two imaging methods (ultrasound, CT, and MRI) and 15 uninvolved healthy volunteers (without physical and psychological diseases from the people of a regular healthy physical examination every year by detecting the blood, urine and fecal routine, liver function, biochemical analysis, hepatitis markers, chest X-ray, abdominal ultrasound and so on) were acquired.Fecal sample collection was performed by using a TinyGene fecal collection box according to the manufacturer’s instructions (TinyGene, Shanghai), and the boxes were placed on ice as soon as possible and stored at -80℃ before further analysis.The 46 samples were subjected to library preparation (including genomic DNA extraction, PCR amplification, recovery using the AxyPrep DNA Gel Extraction Kit, and real-time fluorescence quantification on the FTC-3000TM real-time PCR instrument), followed by Illumina high-throughput sequencing and bioinformatics analysis.The 16S rRNA gene was amplified using primers 515F 5’-GTGCCAGCMGCCGCGGTAA-3’ and 926R 5’-CCGTCAATTCMTTTGAGTTT-3’ targeting the V5-V6 hyper-variable regions and sequenced in the Illumina platform following the manufacturer’s protocols. The sequencing data analysis was performed by using software of Trimmomatic, FLASH and Mothur V.1.39.5 according to the protocol. The Reads obtained by Illumina Miseq sequencing were distinguished according to the barcode, dereplicated and single Reads were discarded, and then filtered Reads were clustered into operational taxonomic units (OTU) assuming 97% similarity, and the optimized sequence was obtained finally. Each OTU was taxonomically assigned using Uclust considering a minimum percentage of similarity to a reference database (Silva 128 and Greengene) match of 90%.