 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 05, 2022 |
| Title |
LowCariesRisk-1 |
| Sample type |
SRA |
| |
|
| Source name |
Dental plaque and saliva
|
| Organism |
human oral metagenome |
| Characteristics |
tissue: Dental plaque and saliva
sampleID: 112143989
subject: B11
caries risk: LowCariesRisk
visit: Day14
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The samples were first lysed using bead-beating, and DNA was extracted in a class 1000 clean room by a guanidine thiocyanate silica column-based purification method using a liquid-handling robot. PCR amplification of the 16S rRNA genes was performed with primers containing universal primers amplifying the V4 variable region (515F: GTGCCAGCMGCCGCGGTAA and 806R: GGACTACHVGGGTWTCTAAT). The primers contained Illumina tags and barcodes. Samples were barcoded with a unique combination of forward and reverse indexes allowing for simultaneous processing of multiple samples. PCR products were pooled, column-purified, and size-selected through microfluidic DNA fractionation.
Consolidated libraries were quantified by quantitative real-time PCR using the Kapa Bio-Rad iCycler qPCR kit on a BioRad MyiQ
16S rRNA gene sequencing
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
qiime2: DADA2, denoising, qiime2 version: 2021.4
qiime2: feature-table plugin, feature table generation
qiime2: phylogeny plugin, rooted-tree generation
R and phyloseq library, phyloseq object creation, R version: R version 4.1.2, Package Phyloseq versin: 1.38.0
Assembly: HOMD_16S_rRNA_RefSeq_V15.22
Supplementary files format and content: feature count in txt file
|
| |
|
| Submission date |
Apr 01, 2022 |
| Last update date |
Apr 05, 2022 |
| Contact name |
Dawud abduweli uyghurturk |
| E-mail(s) |
dawud.abduweliuyghurturk@ucsf.edu
|
| Organization name |
UCSF
|
| Street address |
513 Parnassus Ave.
|
| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL32111 |
| Series (1) |
| GSE199991 |
Dental caries as a risk factor for bacterial blood stream infection (BSI) in children undergoing hematopoietic cell transplantation (HCT) |
|
| Relations |
| BioSample |
SAMN27184113 |
| SRA |
SRX14697334 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
