Ontology highlight
ABSTRACT:
PROVIDER: PRJNA943158 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:DNA extraction method targeted loci environmental
| PRJNA315949 | ENA
Project description:We provide raw gene sequences of 174 flowering time regulatory genes and gene othologs across a large barley population (895 barley lines) selected from a collection of landrace, cultivated barley, and research varieties of diverse origin. This set represents the whole variety of cultivated barley lifeforms, namely two- and six-row genotypes with winter, spring, and facultative growth habits. We applied a target capture method based on in-solution hybridization using the myBaits® technology (Arbor Biosciences, Ann Arbour, MI, USA) which is based on in-solution biotinylated RNA probes. Baits were designed for flowering time regulatory genes and gene othologs, and used for production of 80mer capture oligonucleotides for hybridization. Genomic DNA was extracted from leaves of a single two-week old barley plant per variety using the cetyl-trimethyl-ammonium bromide (CTAB) method. Physical shearing of genomic DNA was performed with an average size of 275 bp. Library preparation was conducted with KAPA Hyper Prep Kit (KAPA Biosystems, Wilmington, MA). Hybridization of customised RNA baits with capture pools was performed at 65°C for 24 hours. Each pooled sequence capture library was sequenced on an Illumina HiSeq3000 instrument using three lanes to generate paired-end reads per sample. Genome sequencing was conducted at AgriBio, (Centre for AgriBioscience, Bundoora, VIC, Australia).
2019-02-15 | E-MTAB-7362 | biostudies-arrayexpress
Project description:This dataset introduces a new protocol called DNase-capture, a method that focuses DNase-seq analysis on selected genomic regions, resulting in a substantial increase in region-specific sequencing coverage. DNase-seq takes advantage of the preferential cutting of DNase I. DNase-capture enhances the resolution of DNase-seq by mixing a DNase-seq library with biotin-tagged bait RNA sequences that are complementary to regions of interest. In a hybridization reaction, target DNA is captured away from background DNA through streptavidin bead binding, and the captured target DNA is sequenced.
2017-10-27 | GSE106217 | GEO
Project description:An anthropogenic chemical contaminant commonly identified in aquatic receiving environments is the non-steroidal anti-inflammatory drug (NSAID), ibuprofen(IBF). While the role of ibuprofen in target organisms is known, there exists a paucity of data on the impact of exposure to non-target wildlife species. In the case of frog species, normal development and environmental fitness involves the actions of the thyroid hormones (THs), particularly at key points in the life cycle. We investigated whether exposure of premetamorphic North American bullfrog (Rana catesbeiana) tadpoles to IBF altered their response to treatment with an exogenous dose of thyroid hormone (T3). Six animals randomly selected from each treatment were examined for the status of the hepatic transcriptome using MAGEX DNA array analysis.
2014-09-23 | E-GEOD-53565 | biostudies-arrayexpress