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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 24, 2020 |
| Title |
B19-0033_2019044582019 |
| Sample type |
SRA |
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| Source name |
Mouse feces
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| Organism |
feces metagenome |
| Characteristics |
host organism: C9orf72 loss of function mouse
bacterial metagenome source: feces
batch id: B19-0033
mouse id: JHU-350
mouse sex: M
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| 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
16S rDNA
B19-0033 Processed
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| 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
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| 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
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| Organization name |
Harvard University
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| Department |
HSCRB
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| Lab |
Eggan
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| Street address |
7 Divinity Avenue SF 258
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| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02138 |
| Country |
USA |
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| Platform ID |
GPL24116 |
| Series (1) |
| GSE147325 |
16s rDNA sequencing of feces from C9orf72 loss of function mice |
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| Relations |
| BioSample |
SAMN14428225 |
| SRA |
SRX7972555 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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