In de novo genome sequencing, mate-pair reads are crucial for scaffolding assembled contigs. However, preparation of mate-pair libraries is not a trivial task, even when using one of the latest approaches, the Nextera Mate Pair Sample Prep Kit from Illumina. To reduce cost and enhance library yield and fidelity when using this kit, we have modified the manufacturer's protocol based on (i) varia...

In the present study, we used Illumina sequencing technology (HiSeq 2000) to sequence the transcriptome of barley (Hordeum vulgare L., cv. Morex) under three different heavy metal stress conditions: copper, zinc and cadmium. For each of those metals, the concentration causing a 50% inhibitory effect for root growth (EC50) was determined. We sequenced the total RNA of both roots and shoots from ...

Mangosteen (Garcinia mangostana L.) has exceptional potential for commercial and pharmaceutical applications due to its delicious fruit and medicinal properties. Nevertheless, the molecular mechanism of mangosteen seed development is poorly understood. In this study, we performed transcriptomic analysis of four seed developmental stages; eight, ten, twelve and fourteen weeks after anthesis. Ill...

There are multiple platforms available for whole-exome enrichment and sequencing (WES). This protocol is based on the Agilent SureSelect Human All Exon platform, which targets ∼50 Mb of the human exonic regions. The SureSelect system uses ∼120-base RNA probes to capture known coding DNA sequences (CDS) from the NCBI Consensus CDS Database as well as other major RNA coding sequence databases, su...

Methods The exons of the NLRP3 gene were amplified via PCR from genomic PBMC DNA. The obtained PCR products were sequenced with an Illumina HiSeq platform. For SNP calling we used the GATK pipeline of the 1000 Genome Project, if the coverage attained 40,000 fold. In order to prove the accuracy of the method, we quantified dilutions of a known heterozygous mutation (T348M) mixed with wildtype DN...

Exome sequencing Genomic DNA was isolated using the Qiagen Blood/Tissue kit (Qiagen, Valencia, CA). Exome capture was performed with the Agilent SureSelect All-Exon v2 kit, and 100 bp paired-end library reads were generated on Illumina HiSeq 2000 to a 50-fold target average depth of coverage. Alignment of reads to the human genome was performed with DNAnexus (www.dnanexus.com) and bwa (Li and D...

In eukaryotes, nucleosomes participate in all DNA-templated events by regulating access to the underlying DNA sequence. However, nucleosome dynamics during a genome response have not been well characterized [1,2]. We stimulated Drosophila S2 cells with heat-killed Gram-negative bacteria Salmonella typhimurium, and mapped genome-wide nucleosome occupancy at high temporal resolution by MNase-seq ...


 Many differentially expressed genes associated with feather colour in quail embryos can be screened using RNA-seq technology. The aim of this study was to verify the accuracy RT-qPCR. transcriptome embryonic skin tissues quails were sequenced by Illumina HiSeq TM2000 sequencing platform. As a result, 2512 found. Among them, 950 up-regulated white-feather embryos, and 1562 down-regulated....

Salinity is a major threat to the yield and productivity of cotton seedlings. In present study, we developed BC 2 F population plants from Gossypium darwinii (5–7) hirsutum (CCRI 12–4) salt-susceptible parents identify salt-resistant candidate genes. The Illumina HiSeq™ strategy was used with bulked segregant analysis. Salt-resistant DNA bulks were pooled by using 30 population. Next-generation...