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Sample GSM4426053 Query DataSets for GSM4426053
Status Public on Mar 24, 2020
Title N20-0002_2020009167028
Sample type SRA
 
Source name Mouse feces
Organism feces metagenome
Characteristics host organism: C9orf72 loss of function mouse
bacterial metagenome source: feces
batch id: N20-0002
mouse id: H->H FTx-10
mouse sex: F
Extracted molecule genomic DNA
Extraction protocol DNA was isolated by Powersoil (QIAGEN, Germantown, MD) per the manufacturer’s protocol and recovery yield and DNA quality was determined by fluorometric analysis.
DNA concentration was standardized and amplified using 16s rRNA primers spanning the V3 and V4 regions (Illumina). Resulting amplified PCR products were analyzed on a Bioanalyzer (Agilent Technologies, Santa Clara, CA) then purified and amplified with primers containing unique sample nucleotide barcodes (Illumina). PCR products were analyzed with the Bioanalyzer for product quality control and also by SYBR green PCR to determine the quantity. All samples were pooled and standardized to a final concentration of 4.0 nM representation for each sample. The 16S PCR product pool was denatured with sodium hydroxide then adjusted to 4.0 pM and combined with 5% PhiX control DNA prior to loading onto a sequencing flow cell (Illumina) with 300 bp paired ends and a unique molecular tag for each sample.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
Description 16S rDNA
N20-0002 Processed
Data processing Library strategy: 16S rDNA-sequencing
Following the sequencing run, the sequence data was separated based on the nucleotide bar code and then compared to the Greengenes database (http://greengenes.lbl.gov)
Relative abundance, alpha diversity, beta diversity and principal coordinate analysis was performed using QIIME analysis software
Genome_build: One Codex Targeted Loci Database (https://app.onecodex.com/references)
Supplementary_files_format_and_content: relative abundances
 
Submission date Mar 20, 2020
Last update date Mar 25, 2020
Contact name Aaron Burberry
E-mail(s) aaron_burberry@harvard.edu, aaronburberry@fas.harvard.edu
Organization name Harvard University
Department HSCRB
Lab Eggan
Street address 7 Divinity Avenue SF 258
City Cambridge
State/province Massachusetts
ZIP/Postal code 02138
Country USA
 
Platform ID GPL24116
Series (1)
GSE147325 16s rDNA sequencing of feces from C9orf72 loss of function mice
Relations
BioSample SAMN14428200
SRA SRX7972574

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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