Fungi and Archaea sequences (D1/D2 and 16S rRNA) from Bos taurus indi... - SRA

SRX3747519: Fungi and Archaea sequences (D1/D2 and 16S rRNA) from Bos taurus indicus vaginal tract: cow of Gyr breed
1 ILLUMINA (Illumina MiSeq) run: 443,569 spots, 170.8M bases, 91.5Mb downloads

Design: Wash samples were lyophilized to reduce sample volume and total DNA was extracted using DNeasy Blood & Cell Culture DNA Midi Kit (Qiagen, Hilden, Germany). This DNA was used as template to perform PCR reactions using universal primers for Archaea (300fEyAr: AGC RRG AGC CCG GAG ATG G; 954rEyAr: CGG CGT TGA RTC CAA TTA AAC) and Fungi (NL1: GCA TAT CAA TAA GCG GAG GAA AAG; NL4: GGT CCG TGT TTC AAG ACG G). For Archaea: a mix containing 25 pmol of each primer, 45 l of Taq Platinum Supermix (Thermo Fischer Scientific, Waltham, USA), 80 ng of template DNA and nuclease-free water to a final volume of 50 l was subjected to the following cycling: 94 C for 4 minutes, 35 cycles of 94 C for 30 seconds, 60 C for 30 seconds, 72 C for 40 seconds and finally 72 C for 10 minutes. For Fungi: a mix containing 10 pmol of each primer, 12.5 l of 2x GoTaq Green Master Mix (Promega), 40 ng of template DNA and nuclease-free water to a final volume of 25 l was subjected to the following cycling: 95 C for 2 minutes, 35 cycles of 95 C for 15 seconds, 54 C for 25 seconds, 72 C for 20 seconds and finally 72 C for 10 minutes. Samples were submitted to a random fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina), DNA fragments were coupled to specific adapters using TruSeq Nano DNA Library Preparation Kit (Illumina, San Diego, USA). Next, the DNA-adapter molecules were purified and submitted to amplification reactions using specific primers targeting the adapters. Amplification products were quantified by real time PCR using the SYBR Fast qPCR Kit (Kapa Biosystems, Wilmington, USA). The libraries were then diluted in a Tris-HCl and 0.1% Tween solution, deposited on a flow cell and subjected to 600 sequencing cycles (2 x 300 bp) using the MiSeq Reagent Kit v3 (Illumina).

Submitted by: Universidade Federal de Minas Gerais

Study: Vaginal microbiota composition of Gyr cattle (Bos taurus indicus)

PRJNA435944 • SRP133595 • All experiments • All runs

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This study aims to describe and characterize vaginal microbiota of healthy cows and heifers of gyr breed Gyr cattle, the Zebuine breed most used in dairy production in Brazil, composed by animals that are capable of maintaining good production standards under different management systems and climates using 16S rRNA for Bacteria and Archaea and D1/D2 region for Fungi.

Sample:

SAMN08606545 • SRS3003929 • All experiments • All runs

Organism: vaginal metagenome

Library:

Name: Cow2_Fungi_Archaea_Metagenomic_Vaginal_tract

Instrument: Illumina MiSeq

Strategy: AMPLICON

Source: METAGENOMIC

Selection: RANDOM PCR

Layout: PAIRED

Runs: 1 run, 443,569 spots, 170.8M bases, 91.5Mb

Run	# of Spots	# of Bases	Size	Published
SRR6788242	443,569	170.8M	91.5Mb	2018-02-27

ID:: 5166451

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