PREDICT
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Homo sapiens
SUBMITTER:
PROVIDER: E-ERAD-16 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The DMDD Programme (Deciphering the Mechanisms of Developmental Disorders ) provides a free online database of morphological and molecular phenotypes from embryonic-lethal mouse gene knockouts (http://www.dmdd.org.uk/). Embryos are imaged using high-resolution episcopic microscopy (HREM), placentas are examined by histology and mutant embryo mRNA expression profiles are compared to wild type. To underpin these investigations we have produced a comprehensive time series of gene expression through normal embryo development<br></br>In this study, yotal RNA was extracted from wildtype C57BL/6N sibling embryos with heterozygous parentage from the Mouse Genetics Project (http://www.dmdd.org.uk/) and DNase treated. Stranded RNAseq libraries were constructed using the Illumina TruSeq Stranded RNA protocol with oligo dT pulldown. <br></br> Notes about samples and libraries:<br></br> (1) A combination of litter identifier and embryo identifier within a litter will unambiguously identify a single embryo used in this study. <br></br> (2) There is a margin of error for the somite-stage information (+/- 1 somite) because some embryos could be in between somite stages. <br></br>(3) Sex of the embryos was determined post-RNA-seq by looking at the expression of Xist (strong expression in females only). <br></br>(4) All knockouts in the parents (and hence grandparents) are for embryonic lethal genes. <br></br> (5) There are four biological replicates per somite-stage. <br></br>(6) Complementary data on genotypically wild-type mice with mixed G0 lineage and no history of genetic modification can also be found in ArrayExpress under accession numbers E-ERAD-401 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-ERAD-401 ) and E-ERAD-499 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-ERAD-499 ) respectively.
2015-02-11 | E-ERAD-352 | biostudies-arrayexpress
Project description:The DMDD Programme (Deciphering the Mechanisms of Developmental Disorders, https://dmdd.org.uk/) provides a free online database of morphological and molecular phenotypes from embryonic-lethal mouse gene knockouts (http://www.dmdd.org.uk/). Embryos are imaged using HREM, placentas are examined by histology and mutant embryo mRNA expression profiles are compared to wild type. To underpin these investigations we have produced a comprehensive time series of gene expression through normal embryo development. Total RNA was extracted from somite number staged, second generation genotypically wild type, C57BL/6N embryos of mixed G0 linages from the Mouse Genetics Programme (http://www.sanger.ac.uk/science/collaboration/mouse-resource-portal) and DNase treated. Stranded RNA-seq libraries were constructed using the Illumina TruSeq Stranded RNA protocol with oligo dT pulldown.<br> Notes about samples and libraries: </br><br>(1) A combination of litter identifier and embryo identifier within a litter will unambiguously identify a single embryo used in this study. </br><br>(2) There is a margin of error for the somite-stage information (+/- 1 somite) because some embryos could be in between somite stages. </br><br> (3) All knockouts in the parents or grandparents are for embryonic lethal genes. </br><br>(4) There are four biological replicates per somite-stage, with the exception of the 4-somite embryos (three biological replicates only). Altogether 111 embryos were sourced, of which 14 were sequenced twice to generate enough read depth/coverage. No new libraries were prepared for the repeated sequencing, despite the assays being assigned new ERX* accessions. </br><br> (5) Sex of the embryos was determined post-RNA-seq by looking at the expression of Xist (strong expression in females only). </br><br> (6) Library constructon batch refers to batch of sample handling post RNA-extraction (size selection, PCR amplification during library preparataion). </br><br>(7) Superbatch gathers 17 representative embryos out of the 111 embryos post RNA-extraction, and put them through the library construction pipeline as one single batch. The generated data is intended to be used for normalisation using the remove unwanted variation (RUV) method. </br> <br> This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ .</br>
2015-11-03 | E-ERAD-401 | biostudies-arrayexpress
Project description:The hemibiotrophic fungus Zymoseptoria tritici causes Septoria tritici blotch disease of wheat (Triticum aestivum). Pathogen reproduction on wheat occurs without cell penetration, suggesting that dynamic and intimate intercellular communication occurs between fungus and plant throughout the disease cycle. We used deep RNA sequencing and metabolomics to investigate the physiology of plant and pathogen throughout an asexual reproductive cycle of Z. tritici on wheat leaves. Over 3,000 pathogen genes, more than 7,000 wheat genes, and more than 300 metabolites were differentially regulated. Intriguingly, individual fungal chromosomes contributed unequally to the overall gene expression changes. Early transcriptional down-regulation of putative host defense genes was detected in inoculated leaves. There was little evidence for fungal nutrient acquisition from the plant throughout symptomless colonization by Z. tritici, which may instead be utilizing lipid and fatty acid stores for growth. However, the fungus then subsequently manipulated specific plant carbohydrates, including fructan metabolites, during the switch to necrotrophic growth and reproduction. This switch coincided with increased expression of jasmonic acid biosynthesis genes and large-scale activation of other plant defense responses. Fungal genes encoding putative secondary metabolite clusters and secreted effector proteins were identified with distinct infection phase-specific expression patterns, although functional analysis suggested that many have overlapping/redundant functions in virulence. The pathogenic lifestyle of Z. tritici on wheat revealed through this study, involving initial defense suppression by a slow-growing extracellular and nutritionally limited pathogen followed by defense (hyper) activation during reproduction, reveals a subtle modification of the conceptual definition of hemibiotrophic plant infection.
2015-03-12 | E-MTAB-4116 | biostudies-arrayexpress
Project description: Not available
2014-11-04 | E-MTAB-4123 | biostudies-arrayexpress
Project description:Our analysis provides a comprehensive picture of how P. trichocarpa responds to drought stress at physiological and transcriptome levels which may help to understand molecular mechanisms associated with drought response and could be useful for genetic engineering of woody plants. Drought stress treatment was performed dividing P. trichocarpa plants into the well-watered (WW) group (soil volumetric water content of 40â45 %) and the water-limited group (soil volumetric water content of 10â15 %). Two cDNA libraries constructed separately from the WW and WL groups were subjected to high-throughput Illumina sequencing.
2013-11-20 | E-MTAB-4126 | biostudies-arrayexpress
Project description:Photosynthesis underpins the viability of most ecosystems, with C4 plants that exhibit âKranzâ anatomy being the most efficient primary producers. Kranz anatomy is characterized by closely spaced veins that are encircled by two morphologically distinct photosynthetic cell types. Although Kranz anatomy evolved multiple times, the underlying genetic mechanisms remain largely elusive, with only the maize scarecrow gene so far implicated in Kranz patterning. To provide a broader insight into the regulation of Kranz differentiation, we performed a genome-wide comparative analysis of developmental trajectories in Kranz (foliar leaf blade) and non-Kranz (husk leaf sheath) leaves of the C4 plant maize. Using profile classification of gene expression in early leaf primordia, we identified cohorts of genes associated with procambium initiation and vascular patterning. In addition, we used supervised classification criteria inferred from anatomical and developmental analyses of five developmental stages to identify candidate regulators of cell-type specification. Our analysis supports the suggestion that Kranz anatomy is patterned, at least in part, by a SCARECROW/SHORTROOT regulatory network, and suggests likely components of that network. Furthermore, the data imply a role for additional pathways in the development of Kranz leaves.
2013-07-29 | E-MTAB-4134 | biostudies-arrayexpress
Project description:The classical maize mutant lazy1 (la1), displayed prostrate growth with reduced shoot gravitropism. We compared the transcriptome profile of the third node in la1-ref mutants with those in wild-type plants using RNA-SEQ to examine the genome-wide effect of the ZmLA1 gene. We generated 14.6 and 36.5 million paired-end reads from two biological samples of wild-type and la1-ref mutant plants, respectively.
2013-11-20 | E-MTAB-4196 | biostudies-arrayexpress
Project description:Nitrogen (N), a critical macronutrient for plant growth and development, is a major limiting factor in most agricultural systems. Microarray analyses have been conducted to investigate genome-wide gene expression in response to changes in N concentrations. Although RNA-Seq analysis can provide a more precise determination of transcript levels, it has not previously been employed to investigate the expression of N-starvation-induced genes. We constructed cDNA libraries from leaf sheaths and roots of rice plants grown under N-deficient or -sufficient conditions for 12 h. Sequencing the libraries resulted in identification of 33,782 annotated genes. A comparison of abundances revealed 1,650 transcripts that were differentially expressed (fold-changeââ¥â2) due to an N-deficiency. Among them, 1,158 were differentially expressed in the leaf sheaths (548 up-regulated and 610 down-regulated) and 492 in the roots (276 up, 216 down).
2015-08-30 | E-MTAB-4195 | biostudies-arrayexpress
Project description:A major step in the higher plant life cycle is the decision to leave the mitotic cell cycle and begin the progression through the meiotic cell cycle that leads to the formation of gametes. The molecular mechanisms that regulate this transition and early meiosis remain largely unknown. To gain insight into gene expression features during the initiation of meiotic recombination, we profiled early prophase I meiocytes from maize (Zea mays) using capillary collection to isolate meiocytes, followed by RNA-seq.
2013-07-25 | E-MTAB-4210 | biostudies-arrayexpress
Project description:To discover the transcriptional dynamics during seed germination we have obtained the time course transcriptomes for embryonic shoot apical meristem (SAM) every six hours, starting from dry seeds to hour 72 (3 days).
2013-04-02 | E-MTAB-4205 | biostudies-arrayexpress