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| Status |
Public on Aug 20, 2013 |
| Title |
E1-02-02 |
| Sample type |
SRA |
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| Source name |
Defined bacterial assemblage from a gnotobiotic mouse
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| Organism |
Bacteria |
| Characteristics |
experiment: E1
mouse: 2
days post-colonization: 2
collection site: feces
diet group: LF/HPP=>HF/HS=>LF/HPP
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| 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.
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| Growth protocol |
Bacteria from frozen culture stocks were introduced as an artificial community (AC) into 10-12 week-old male gnotobiotic C57BL/6J mice. Cells were therefore maintained over the course of the experiment within mice until sampling occurred.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from fecal and cecal 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Sample was collected from a gnotobiotic mouse colonized at day 0 with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group' field indicates the order in which the LF/HPP and HF/HS diets were administered.
B. caccae ATCC 43185, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. uniformis ATCC 8492, B. vulgatus ATCC 8482, B. cellulosilyticus WH2, C. scindens ATCC 35704, C. spiroforme DSM 1552, C. aerofaciens ATCC 25986, D. longicatena DSM 13814, P. distasonis ATCC 8503, R. obeum ATCC 29174
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| 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. in a previous publication (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: AAVM00000000.2, AAXF00000000.2, AE015928.1, AAYH00000000.2, CP000139.1, ABFY00000000.2, ABIK00000000.2, AAVN00000000.2, AAXB00000000.2, CP000140.1, AAVO00000000.2; note that one additional genome included in the analysis (that of B. cellulosilyticus WH2) was sequenced as part of this study and has not yet been assigned an NCBI accession number.
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.
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| Submission date |
Jun 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Nathan P McNulty |
| E-mail(s) |
nathan.p.mcnulty@gmail.com
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| Phone |
314-362-3963
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| Organization name |
Washington University School of Medicine
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| Department |
Center for Genome Sciences and Systems Biology
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| Lab |
Gordon
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| Street address |
4444 Forest Park Ave. (5th Floor)
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| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63108 |
| Country |
USA |
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| Platform ID |
GPL11535 |
| Series (2) |
| GSE48193 |
Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome (COPRO-Seq) |
| GSE48537 |
Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome |
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| Relations |
| SRA |
SRX312334 |
| BioSample |
SAMN02211355 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1171985_machineGAII-440_run64_lane4_GTGT_E1-02-02.hitratios.txt.gz |
435 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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