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E-MTAB-2764

ABSTRACT: SNP Discovery in Nine Lines of Cultivated Barley

OTHER RELATED OMICS DATASETS IN: PRJEB5301PRJEB84PRJEB628PRJEB3027

PROVIDER: E-MTAB-2764 | ExpressionAtlas | 2016-01-08

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MTAB-2764-analysis-methods.tsv	Tabular
	E-MTAB-2764-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-2764-coexpressions.tsv.gz	Tabular
	E-MTAB-2764-configuration.xml	Xml
	E-MTAB-2764-configuration.xml.beforeQC	Xml

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Project description:SNP Discovery in Nine Lines of Cultivated Barley

| PRJEB3130 | ENA

SNP Discovery in Nine Lines of Cultivated Barley

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

Microarray of barley genes in wheat-barley chromosome addition lines

Project description:Transcript levels of barley genes were examined in the wheat-barley chromosome addition lines having one of six barley chromomes, 2H, 3H, 4H, 5H, 6H and 7H. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Seungho Cho. The equivalent experiment is BB8 at PLEXdb.]

2011-11-22 | GSE33415 | GEO

Mapping barley genes to chromosome arms by transcript profiling of wheat-barley ditelosomic chromosome addition lines

Project description:We utilized the Barley1 Affymetrix GeneChip for comparative transcript analysis of Betzes barley, Chinese Spring wheat, and Chinese Spring–Betzes ditelosomic chromosome addition lines to physically map barley genes to their respective chromosome arm locations. We mapped barley genes to chromosome arms (1HS, 2HS, 2HL, 3HS, 3HL, 4HS, 4HL, 5HS, 5HL, 7HS, and 7HL) based on their transcript levels in the ditelosomic addition lines. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Hatice Bilgic. The equivalent experiment is BB55 at PLEXdb.]

2011-11-22 | GSE33400 | GEO

Expression profiles of barley chromosome addition lines of common wheat

Project description:Barley contains a much higher content of bioactive substances than wheat. In order to investigate the effect of genome interaction between barley and wheat on phytosterol content, we used a series of barley chromosome addition lines of common wheat. The wheat 38k-microarray was utilized for screening of genes with expression levels specifically increased by an additive effect or synergistic action between wheat and barley chromosomes. We determined the overall expression pattern of genes related to phytosterol biosynthesis in wheat and in each addition line. Together with determining the phytosterol levels of wheat, barley and each addition line, we assess the critical genes in the phytosterol pathway that can be expressed to promote phytosterol levels.

2011-12-08 | GSE28023 | GEO

mlo5-mediated resistance responses in barley

Project description:Gene expression of a near-isogenic pair of barley lines differing in absence or presence of the mlo5 resistance gene in response to attack by barley powdery mildew (Bgh). ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Achim Fischer. The equivalent experiment is BB7 at PLEXdb.]

2011-11-22 | GSE33406 | GEO

Gene expression patterns within cell lines are predictive of chemosensitivity

Project description:We generated RNA's and measured expression of 40000 genes using spotted cDNA microarrays from the fifty nine publicly available cell lines of the NCI Developmental Therapeutics Program's NCI60 studies and an additional set of seven cell lines for which GI50 compound sensitivity data were available. All cell lines were grown to 80% confluence in RPMI 1640 supplemented with phenol red, glutamine (2 mM) and 5% fetal calf serum. This expression data, in conjunction with the compound sensitivity data sets available from the DTP, were used to empirically determine whether gene-compound correlates of a sufficiently high correlation coefficient would have a suitable low false discovery rate to support the use of a correlative approach and these datasets for early discovery approaches for new targeted therapies. A cell type comparison design experiment design type compares cells of different type for example different cell lines. Keywords: cell type comparison design

2008-02-08 | GSE7947 | GEO

Basal expression of nine pancreatic cancer cell lines

Project description:Basal expression of nine pancreatic cancer cell lines

| PRJNA673194 | ENA

Targeted resequencing of phenology genes in a diverse panel of barley varieties

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

Transcriptomic changes in the crown (stem base) of barley (Hordeum vulgare L. cv. Golden Promise) during crown-root initiation and development

Project description:Purpose: The goal of this study was to investigate the mechanisms involved in the initiation and development of crown-roots (CRs) in barley and to estimate the role of cytokinins (CKs) in this process. Method: stranded libraries were obtained from RNA extracted from the stem base of 1 day-after-germination (DAG) and 10DAG-seedlings of wild-type (WT) and AtCKX-overexpressing barley lines (OE-CKX). OE-CKX lines have a reduced content of endogenous CKs and are characterized by a higher number of CRs. Libraries were deep sequenced on Illumina HighSeq platform. Each sample was investigated in three independent biological replicates. Results: Using a data analysis workflow optimized for barley, we identified more than 4000 transcripts differentially expressed in the stem base of 1DAG and 10DAG-seedlings. Expression as determined by RNA-seq was validated by real-time PCR. Our data were compared to the transcriptomic profiling obtained from rice and we were able to identify genes potentially involved in the initiation/development of CRs in barley. Also the use of the transgenic line with altered endogenous CK content allowed us to conclude about the role of CKs in the process. Conclusions: Our study represents the first analysis aiming to understand the initiation and development of CRs in barley.

2016-11-01 | GSE87737 | GEO

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