Truseq sbs kits v3

Each of the 16 DNAs from Alpine, Creole or Saanen goat was sequenced independently on an Illumina HiSeq2000 machine using one lane for each animal. 3µg of DNA was used for each animal to construct libraries following manufacturer’s protocol (Illumina TruSeq DNA sample prep). Then, libraries were quantified and sequenced on one lane for each on an Illumina HiSeq2000 sequencer using standard Illumina protocol (TruSeq SBS kits v3), with 100 bp paired-end reads and ∼250 bp insert length.
Two genomic DNA pools were made for meat goats: pool 1 from 20 Boer goats and pool 2 from 20 Savanna goats and 24 Katjang goats. Each DNA sample was quantified three times (using Hoechst dye and fluorometer) and equal amount of genomic DNA from each sample based on the average concentration of the three readings were used to make DNA pools. The pools were whole genome shotgun sequenced on an Illumina Genome Analyzer IIx machine using the standard Illumina protocol, with 78 bp paired-end reads and ∼300 bp insert length.
The genomic RRLs of the 17 Dutch Saanen bucks (AluI and HhaI) were combined and prepared using the Illumina Sample Preparation kit [20] and sequenced with the Illumina GAII, Illumina Inc., USA with 76 bp paired end reads.
Access to high-throughput sequences can be requested from research teams and subjected to signing of a Data Transfer Agreement.

For the RNA-Seq analysis, the fruit were ground using an homogeniser (Ultra-Turrax T25; Janke and Kunkel IKA-Labortechnik, Staufen, Germany), and the total RNA was extracted from 1 g of the frozen-powder homogenate, according to Landi et al. (2014) (link). The RNA quantity and quality were determined using a Nanodrop 2000 (Thermo Fisher Scientific Inc., Wilmington, DE, USA) and a bioanalyzer (model 2100; Agilent Technologies, Santa Clara, CA, USA). cDNA libraries were prepared from 4 μg total RNA using TruSeq RNA Sample Preparation kits v2 (Illumina, Inc., San Diego, CA, USA), and validated according to the Illumina low-throughput protocol. After normalization, the cDNA libraries were pooled for multiplexing, before loading onto a flow cell (five samples per lane). The hybridization and cluster generation were performed on a cBot System using TruSeq SR Cluster kits v3 (Illumina). The sequencing was performed with an Illumina HiScanSQ platform, using TruSeq SBS kits v3 (Illumina) to obtain single reads 50 nt in length. The indexed raw sequencing reads from each library were de-multiplexed using the CASAVA v1.8 software (Illumina).