|
| Status |
Public on May 20, 2011 |
| Title |
9_HF_HP_noDP_noRh [COPRO-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
mouse feces
|
| Organisms |
[Clostridium] symbiosum; Bacteroides thetaiotaomicron VPI-5482; Bacteroides ovatus ATCC 8483; Bacteroides caccae ATCC 43185; Collinsella aerofaciens ATCC 25986; Marvinbryantia formatexigens DSM 14469; Escherichia coli str. K-12 substr. MG1655; Agathobacter rectalis ATCC 33656 |
| Characteristics |
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 8-gut bacteria
diet: Mouse was fed Harlan Teklad Diet TD.09057.
|
| Growth protocol |
Fecal samples obtained from mice were span frozen in liquid nitrogen and stored at -80°C and maintained at this temperature prior to processing.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fecal samples obtained from mice were immediately frozen in liquid nitrogen and stored at -80 °C until processing. All of the samples were suspended in a solution containing 500 ul of acid-washed glass beads (Sigma-Aldrich), 500 ul of extraction buffer A (200 mM Tris [pH 8], 200 mM NaCl, 20 mM EDTA), 200 ul of 20% SDS, and 500 ul of a mixture of phenol:chloroform:isoamyl alcohol (25:24:1, pH 8.0; Ambion) and lysed by using a bead beater (BioSpec Products). Cellular debris was removed by centrifugation (8,000g; 3 min). The nucleic acids were precipitated with isopropanol and sodium acetate and resuspended in 100 ul TE. The resuspension was further purified with a Qiagen PCR column and eluted into 30 ul of EB buffer.
Libraries were prepared according to Illumina's instructions accompanying the genomic DNA Sample Kit. Briefly, gDNA was sonicated in a biorupter sonicator, cleaned up/concentrated through a Qiagen PCR column, and end-repaired. The blunt DNA was treated with Klenow fragment (exo minus) to add an A-overhang, and ligated to the relevant Illumina adapter sequence (either with our without a barcode). Adaptered-DNA was then size-selected on a agarose gel and PCR amplified. The purified PCR was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.library strategy
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Fecal pellet from a mouse (c57Bl6) colonized with 8-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09057.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
|
| Data processing |
After dividing sequence runs by barcode, we mapped the reads to the relevant genomes using the ssaha2 algorithm. Minimum score thresholds for ssaha were selected based on the distribution of scores for all mapped reads of a 32nt barcoded sample and a 36-nt non-barcoded sample (29 was selected as the minimum score for 32nt barcoded samples; 33 was the minimum score used for 36-nt non-barcoded samples). Although an 18-nt read is sufficient to map more than 90% of the sequencing reads, even at 32-36nt there is a large fraction of the reads that map to multiple locations within a genome or across genomes. Reads that map non-uniquely were discarded.
|
| |
|
| Submission date |
Jan 31, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeremiah J Faith |
| E-mail(s) |
faithj@wustl.edu
|
| Organization name |
Washington University in St. Louis
|
| Street address |
Campus Box 8510
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63108 |
| Country |
USA |
| |
|
| Platform ID |
GPL11535 |
| Series (1) |
| GSE26687 |
Predicting a human gut microbiota's response to diet in gnotobiotic mice. |
|
| Relations |
| SRA |
SRX040073 |
| BioSample |
SAMN00199638 |
