Project description:RNA sequencing of peripheral immune cells from patients +/- an IBD risk variant. Peripheral immune cells +/- in vitro test compound treatment.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/
Project description:Effect of low-doses of ionizing radiation on the behaviour of epithelial cells. The aim of the study is to check whether a single exposure of 50 mGy of ioninzing radiation promotes changes in RNA transcription levels and/or mutations.
Project description:The Arabidopsis Branching Enzyme 1 (BE1) gene encodes a putative glycoside hydrolase involved in carbohydrate metabolism. A partial loss-of-function mutation of the BE1 gene (be1-3 mutant) severely impaired adventitious shoot formation and somatic embryogenesis but not root formation in tissue culture. To gain a better understanding of the molecular mechanism underlying the in vitro plant regeneration defects caused by the BE1 gene mutation, we performed RNA sequencing analysis (RNA-seq) to examine the differential gene expression between WS and be1-3 mutant at dedifferentiation and redifferentiation stages.
Project description:The concurrent epigenetic changes during this period of remarkable improvement in maize grain yield remain unknown. Here, we performed MethylC-seq and RNA-seq on 4 related inbred lines with known pedigree information. Analysis of epigenetic changes over the course of historical maize breeding is a valuable new avenue in the exploration for crop improvement. These data lead us to suggest that novel epihaplotypes, in addition to DNA variation, are a substrate of selection during breeding, and that epigenetic variation between parents may also contribute to heterosis in hybrids. Xie, S; et al. 2013. Maize Genetics Conference Abstracts. 54:P326
Project description:Maize exhibits levels of structural variation (SV) of non-repeat sequences that are unprecedented among higher eukaryotes. This SV includes hundreds of copy number variants (CNVs) and thousands of presence/absence variants (PAVs). Many of the PAVs contain intact, expressed, single-copy genes that are present in one haplotype but absent from another. The goal of this project is to test the hypothesis that differences in gene copy number (both gains and losses) contribute to the extraordinary phenotypic diversity and plasticity of maize. Maize is a good model for these studies because it exhibits a rapid decay of linkage disequilibrium (LD) and because a draft genome sequence of the B73 inbred and mapping populations are available. As a first step, the Zeanome, a near-complete set of genes present in B73, other maize lines and the wild ancestor of maize (teosinte), is being defined using transcriptomic data. Note: All samples in SRA were assigned the same sample accession (SRS302561). This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
Project description:For this project, we have sequenced, assembled and annotated a transcriptome of a diploid wheat Triticum urartu accession PI 428198. The sequencing libraries were prepared from shoot and root tissues harvested from 2-3 week old seedlings. All sequencing was carried out on the Illumina HiSeq platform using the 100 bp pair-end protocol (248.5 million reads). The assembly was constructed using a multiple k-mer approach with a de novo assembly algorithm implemented in CLC Genomics Workbench 5.5 and additional redundancy reduction with CD-HIT and blast2cap3 programs. Open reading frames and proteins were predicted using BLASTX searches and a findorf algorithm.
Project description:To determine transcriptome dynamics regulated by CPL3 during elicitation of immune responses, we performed RNA sequencing (RNA-seq) analysis of Col-0 WT and cpl3-3 mutant treated without or with flg22 for 30 min.
Project description:We used RNA-Seq to systematically investigate the global transcriptomes of rice which was inoculated with viruliferous SBPH, or inoculated with insect-derived RSV or plant-derived RSV by mechanical inoculation, and generated a useful resource for the immune reaction of rice in face of different kinds of RSV. The changes in the expression of candidate transcripts may provide valuable information for future studies on molecular mechanisms of rice stripe disease.
Project description:This study used with RNA-Seq to examine the tissue specific expression data within sorghum plants for improving the Sorghum bicolor gene annotation. We examined the RNA from tissues (spikelet, seed and stem) in Sorghum bicolor (BTx623).Total RNAs form each tissues were extracted using SDS/phenol method followed by LiCl purification