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Sample GSM4125401

Query DataSets for GSM4125401

Status

Public on Oct 17, 2019

Title

CK114 - NH

Sample type

SRA

Source name

Cervico-vaginal lavage

Organism

Homo sapiens

Characteristics

tissue: Cervico-vaginal lavage
material sequenced: 16S rRNA gene
group: NH

Extracted molecule

genomic DNA

Extraction protocol

Genomic DNA was extracted from the CVL supernatants using a modified DNA isolation method as described in Stearns et al. (Stearns et al., 2015). CVL supernatants were inverted to mix and transferred to screw cap tubes containing 2.8mm ceramic beads, 0.1mm glass beads, GES, and sodium phosphate buffer. Samples were bead beat and centrifuged as described in Stearns et al., 2015 and the resulting supernatant was further processed using the robotic MagMAX Express 96-Deep Well Magnetic Particle Processor (Applied Biosystems, Foster City, CA) with the Multi-Sample kit (Life Technologies #4413022, Burlington, Canada).
sl1p pipeline (Whenlan and Surette, 2017, BMC Microbiome)
16S rRNA gene sequencing

Library strategy

RNA-Seq

Library source

genomic

Library selection

cDNA

Instrument model

Illumina MiSeq

Data processing

Paired-end alignment using PANDAseq
FASTQ Trimming using Cutadept/sickle
FASTQ Culling using Chimera checking
OTU picking - de novo (AbundantOTU+, CD-HIT, DNACLUST, UCLUST, UPARSE) and closed reference (BLAST, UCLUST-ref, UCLUST-ref-strict)
Genome_build: Taxon Assignment - assigment algorithm (BLAST, RDP) and reference database (Greengenes 2011, Greengenes 2013, Silva 111)

Submission date

Oct 16, 2019

Last update date

Oct 17, 2019

Contact name

Jocelyn M Wessels

Organization name

McMaster University

Department

Obstetrics and Gynecology

Street address

1280 Main Street West