Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR150449.cram | Other | |||
| ERR150449.cram.crai | Other | |||
| ERR150449.fastq.gz | Fastqsanger.gz | |||
| ERR150450.fastq.gz | Fastqsanger.gz | |||
| ERR150451.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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Project description:SNP Discovery in Nine Lines of Cultivated Barley
2016-01-08 | E-MTAB-2764 | ExpressionAtlas
Project description:Barley (Hordeum vulgare L.) is amongst the oldest domesticated crop plants and remains one of the world's most important crop species. It is diploid with a haploid genome of 5.1 gigabases (Gb), twice the size of those of human and maize, and closely related to the most widely grown crop, hexaploid wheat. To meet global demand for food, feed and fibre, it is commonly agreed that reference genome sequences of our crop plants are urgently required to enable genome-assisted crop improvement. As part of the The International Barley Genome Sequencing Consortium (IBSC) we present here raw data obtained from Illumina (GAII) sequencing of RNA samples from nine different barley cultivars for the purpose of Single Nucleotide Polymorphism (SNP) discovery.
2012-11-28 | E-MTAB-2764 | biostudies-arrayexpress
Project description:To provide comprehensive spatiotemporal information about biological processes in developing grains of cultivated barley (Hordeum vulgare subsp. vulgare), we performed a chromatin immunoprecipitation of H3K27me3 followed by high-throughput sequencing (ChIP-seq) in barley endosperm at 16 days after pollination.
2023-07-26 | GSE238237 | GEO
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:We hypothesized that the genome segments of cultivated barley should show certain similarity with its ancestral wild barley. Instead of whole genome sequences, we employed RNA-Seq to investigated the genomic origin of modern cultivated barley using some representative wild barley genotypes from the Near East and Tibet, and representative world-wide selections of cultivated barley.
2014-10-06 | E-MTAB-4221 | biostudies-arrayexpress
Project description:Cultivated carrot (Daucus carota L. ssp. sativus) was domesticated from wild carrot (Daucus carota L. ssp. carota) with radical different traits. The aim of this study was to compare the root transcriptomes between cultivated and wild carrots for SNP discovery, inferring domestication process, and identifying domestication genes. Six cultivated carrots representing main European carrot root types and five wild carrot populations from widely dispersed sites were used. The root transcriptomes were sequenced with multiplexing paried-end sequencing in Illumina Genome Analyzer IIx.
2013-10-24 | E-MTAB-1340 | biostudies-arrayexpress
Project description:To provide comprehensive spatiotemporal information about biological processes in developing grains of cultivated barley (Hordeum vulgare subsp. vulgare), we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from 4 to 32 days after pollination.
2023-07-26 | GSE233316 | GEO
Project description:Genetic/genome diversity underlying variation in seed oil composition and content among soybean varieties is largely attributed to differences in transcript sequences and/or transcript accumulation of oil production related genes in seeds. Discovery and analysis of sequence and expression variations in these genes will accelerate soybean oil quality improvement. In an effort to identify these variations, we sequenced the transcriptomes of soybean seeds from nine lines varying in oil composition and/or total oil content. Our results showed that 69,338 distinct transcripts from 32,885 annotated genes were expressed in seeds. A total of 8,037 transcript expression polymorphisms and 50,485 transcript sequence polymorphisms (48,792 SNPs and 1,693 small Indels) were identified among the lines. Effects of the transcript polymorphisms on their encoded protein sequences and functions were predicted. The studies also provided independent evidence that the lack of FAD2-1A gene activity and a non-synonymous SNP in the coding sequence of FAB2C caused elevated oleic acid and stearic acid levels in soybean lines M23 and FAM94-41, respectively. As a proof-of-concept, we developed an integrated RNA-seq and bioinformatics approach to identify and functionally annotate transcript polymorphisms, and demonstrated its high effectiveness for discovery of genetic and transcript variations that result in altered oil quality traits. The collection of transcript polymorphisms coupled with their predicted functional effects will be a valuable asset for further discovery of genes, gene variants, and functional markers to improve soybean oil quality. transcriptome comparison of nine different soybean varieties
2016-01-13 | E-GEOD-56297 | biostudies-arrayexpress
Project description:Gasterosteus aculeatus SNP discovery
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