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SRX1851952: 16S rRNA Gene Profiling of Mus Musculus: adult GI microbiome
1 ILLUMINA (Illumina MiSeq) run: 409,399 spots, 161.9M bases, 54.2Mb downloads

Design: DNA was purified from tissue samples using the Qiagen AllPrep DNA/RNA Mini Kit according to the manufacturerŐs recommendations. The V4 region of the 16S rRNA gene was PCR amplified in triplicate reactions using barcoded primers amenable to Illumina equencing. Triplicate reactions were combined, purified using the SequalPrep Normalization Plate Kit (Invitrogen) and pooledin approximately equimolar concentrations. Pooled libraries were sequenced in a 251 x 151bp sequencing run on the MiSeq Desktop Sequencer (Illumina). Downstream processing of sequencing reads was performed as follows: paired sequencing reads were assembled using FLASh followed by quality filtering and demultiplexing using QIIME. Open reference OTU picking was used to cluster demultiplexed sequencing reads at 97%, chimeras were identified using ChimeraSlayer and removed and taxonomy was assigned based on the Greengenes database.
Submitted by: University of California, San Francisco
Study: Dvl1 regulates gut microbiota composition
show Abstracthide Abstract
Homeostasis of the gastrointestinal (GI) tract is controlled by complex interactions between epithelial and immune cells and the resident microbiota. Here, we studied the role of Wnt signaling in GI homeostasis using Dvl1–/– mice, which display aberrant GI transit. Dvl1–/– mice exhibit a significantly distinct GI microbiota, and manipulation of the gut microbiota in mutant mice rescued the GI transit abnormality. Moreover, manipulation of the gut microbiota in wild-type mice induced a GI transit abnormality akin to that seen in Dvl1–/– mice. Together, these data indicate that microbiota manipulation can overcome host dysfunction to correct GI transit abnormalities. Our findings illustrate a mechanism by which the gut microbiota composition promote normal GI function.
Sample: KO.1.ILE.12WK.CO_PLATE_2_A1_TCTGAGGTTGCC
SAMN05256922 • SRS1509305 • All experiments • All runs
Organism: Mus musculus
Library:
Name: KO.1.ILE.12WK.CO
Instrument: Illumina MiSeq
Strategy: AMPLICON
Source: METAGENOMIC
Selection: PCR
Layout: PAIRED
Runs: 1 run, 409,399 spots, 161.9M bases, 54.2Mb
Run# of Spots# of BasesSizePublished
SRR3678243409,399161.9M54.2Mb2016-06-21

ID:
2645867

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