Dataset features

Specifications


Dataset type: Other
Number of samples: 48
Release date: Dec 3 2015
Last update date: Mar 3 2016
Access: Public
Dataset link Gut Microbiota Orchestrates Energy Homeostasis during Cold [16S rRNA gene V4-region miSeq]

Experimental Protocol


C57BL/6J mice were put for 31 day on cold (6C) or room temperature. Fresh feces and cecum samples were collected, immediately frozen and stored. Bacterial DNA content was extracted using QIAamp Fast DNA stool Mini Kit (Qiagen). Bacterial DNA was PCR amplified with barcoded universal bacterial primers targeting variable regionV4 of 16SrRNA gene. Samples were pooled and sequenced with Ilumina MiSeq platform. Using QIIME and custom scripts, sequences were quality filtered and demultiplexed using exact matches to the supplied DNA barcodes. Resulting sequences were then searched against the Greengenes reference database of 16S rRNA gene sequences, clustered at 97% by uclust. The longest sequence from each Operation Taxonomic Unit (OTU) thus formed was then considered as the OTU representative sequence, and assigned taxonomic classification via Mothur's Bayesian classifier, trained against the Greengenes database clustered at 98%. Each listed sample is indivudual biological replicate.

Repositories


GEO

GSE74227

ENA

SRP065234

BioProject

PRJNA299679

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Contact


Ozren Stojanovic