|
| Status |
Public on Jul 12, 2013 |
| Title |
NoDp3_d14_CS_S3 |
| Sample type |
SRA |
| |
|
| Source name |
Defined bacterial assemblage from the feces of a gnotobiotic mouse
|
| 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 |
experiment: E3
group/diet: 0.12% SO4, 3% Chond. SO4
collection site: Feces
days after colonization: 14
|
| Treatment protocol |
Immediately after collection, samples were subjected to flash-freezing in liquid nitrogen and storage at -80 C until total community DNA extractions could be performed.
|
| Growth protocol |
Bacteria from frozen culture stocks were introduced as an artificial community (AC) into 7-8 week-old male gnotobiotic NMRI mice. Cells were therefore maintained over the course of the experiment within mice until sampling occurred.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from fecal samples using mechanical disruption (bead-beating with 0.1 mm zirconium beads) in phenol:chloroform:IAA in the same manner as described by McNulty et al. in a previous publication (PMID: 22030749).
Libraries were prepared according to a slightly modified version of the protocol accompanying the Illumina Genomic DNA Sample Prep Kit. Briefly, total bacterial gDNA was sonicated in a BioRuptor XL water bath sonicator, cleaned up and concentrated using a Qiagen PCR Purification column, and end-repaired using Klenow DNA polymerase. The blunt DNA was treated with Klenow fragment (exo minus) to add an adenine overhang, and the A-tailed molecules were ligated to the relevant barcoded Illumina adapter sequence. Adaptered-DNA was then size-selected by agarose gel electrophoresis. Fragments of the appropriate size were PCR amplified and purified, after which the purified PCR products were loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer I, II or IIx following the manufacturer's protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Library strategy: COPRO-Seq
Demultiplexing: sequences were demultiplexed by 4 nt barcode, requiring an exact match (sequences without a barcode match were excluded from the analysis)
Trimming: after demultiplexing, all sequences were trimmed to 25 bases to eliminate low-quality bases at the ends of each read
Mapping: sequences were aligned to the reference genomes of the 12 bacteria included in the study using Illumina's ELAND aligner (as provided in GAPipeline-1.4.0). Only perfect, non-redundant matches were carried forward in the analysis.
Normalization: raw counts were normalized based on the informative genome size (IGS) of each organism included in the analysis, as described by McNulty et al (PMID: 22030749).
Summarization: the proportional representation of each organism in the analysis was determined by dividing its normalized counts within a sample by the total normalized counts for all organisms within that sample.
Genome_build: AAVM00000000; AE015928.1; AAVN00000000; ACCL00000000; NC_000913.2; NZ_AAXF00000000.2; NC_012781.1; assembly for C. symbiosum can be found at http://genome.wustl.edu/pub/organism/Microbes/Human_Gut_Microbiome; for D. piger: PRJNA30377
Supplementary_files_format_and_content: Tab-delimited text file. The file header (in angle brackets, <>) specifies the sample from which data were derived. Subsequent rows specify the organism/reference genome, raw counts, normalized counts, and normalized relative proportion for each taxon included in the alignment. Additional details are available in the accompanying 'README.txt' file.
|
| |
|
| Submission date |
Jul 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Federico E Rey |
| E-mail(s) |
reyf@wustl.edu
|
| Phone |
314-963-0284
|
| Organization name |
Washington University
|
| Department |
Pathology
|
| Lab |
Gordon
|
| Street address |
4444 Forest Park Blvd
|
| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63108 |
| Country |
USA |
| |
|
| Platform ID |
GPL17434 |
| Series (2) |
| GSE48807 |
The metabolic niche of a prominent sulfate-reducing human gut bacterium [2] |
| GSE48809 |
The metabolic niche of a prominent sulfate-reducing human gut bacterium |
|
| Relations |
| BioSample |
SAMN02231298 |
| SRA |
SRX320378 |
