Ontology highlight
ABSTRACT:
PROVIDER: PRJNA967221 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
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Project description:A spontaneously phenotypically degenerated strain of M. robertsii strain ARSEF 2575 (M. robertsii lc2575; lc = low conidiation) showed a reduction in conidiation and fungal virulence after successive subculturing on artificial medium. However, the conidial production and fungal virulence of a phenotypically degenerated M. robertsii were recovered by serially passaging through a plant host. The DNA methylation level of phenotypically degenerated Metarhizium robertsii M. robertsii lc2575 and this fungi after solider bean passages were tested through the whole genome bisulfite sequencing. The results showed that approximately 0.379 % of cytosines are methylated in the fungi after bean passages, almost the same as the DNA methylation level in M. robertsii lc2575 (0.375%). The distribution of different methylated regions located more on intergenic regions of fungi after bean passages than M. robertsii lc2575. Gene Ontology (GO) analysis and KEGG analysis of DMR-associated genes revealed that amino acid, carbohydrate and fatty acid metabolism.
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Project description:To dissect the gene regulatory networks operating during Scarlet Runner Bean seed development, we identified the binding sites genome-wide for transcription factor in Scarlet Runner Bean seeds during seed development using ChIP-seq
2020-07-13 | GSE153644 | GEO
Project description:Investigation of whole genome gene expression level changes in two asparagus bean accesions B47 and B128 under drought stress, compared to well-watered conditions. Two organs, leaf and root, were sampled for each accesion under both well-watered and drought conditions.
2014-11-26 | GSE63636 | GEO
Project description:The pod is the main edible part of Phaseolus vulgaris L. (common bean). The commercial use of the pods is mainly affected by their color. Consumers seem to prefer golden pods. However, planters suffer economic losses because of pod color instability. The aim of the present study was to identify the gene responsible for the golden pod trait in the common bean. ‘A18-1’ (a golden bean line) and ‘Renaya’ (a green bean line) were chosen as the experimental materials. Genetic analysis indicated that a single recessive gene, pv-ye, controls the golden pod trait. A candidate region of 4.24-Mb was mapped to chromosome A02 using bulked-segregant analysis coupled to whole genome sequencing. In this region, linkage analysis in an F2 population localized the pv-ye gene to an interval of 182.9-kb between the simple sequence repeat markers SSR77 and SSR93. This region comprised 16 genes in this region, comprising 12 annotated genes from the P. vulgaris database, and 4 functionally unknown genes. Combined with transcriptome sequencing, we identified Phvul.002G006200 as the potential candidate gene for pv-ye. Sequencing of Phvul.002G006200 identified a single nucleotide polymorphism (SNP) in pv-ye. This SNP is located in the coding region and is responsible for substituting a glutamic acid with an glutamine at position 416 of the pv-ye protein (E416Q). A pair of primers covering the SNP was designed and the fragment was sequenced to screen 316 F2 plants with the ‘A18-1’ phenotype, based on the different site. Our findings showed that the among the 316 mapped individuals, the SNP cosegregated with the ‘A18-1’ phenotype. The findings presented here could form the basis to reveal the mechanism of the golden pod trait in the common bean at the molecular level.
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Project description:250 adult T. urticae females from the London strain (grown on acyanogenic P. vulgaris cv. Prelude bean plants) were transferred to cyanogenic P. lunatus cv. 8078 bean plants. Thirty-five generations after the host transfer, total RNA was extracted from mites growing on both bean species (London and London-CYANO strain) and used in in a genome-wide gene expression microarray (Sureprint G3 microarray, Agilent) experiment to assess significantly differentially expressed genes (FC ≥ 2 and FDR-corrected p-value < 0.05) between mites grown on P. vulgaris (cv. Prelude) bean plants (London strain) and mites grown for 35 generations on P. lunatus (cv. 8078) bean plants (London-CYANO strain).
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Project description:We used our newly ultra deep sequence data and bioinformatics to re-annotate P. xylostella genome for high confidence miRNAs with the correct 5p and 3p arm features. Furthermore, the whole genome was screened to identify potential miRNA binding sites using three target-predicting algorithms. Totally, 203 mature miRNAs were annotated, including 33 novel miRNAs. Two geographical populations of Diamondback moth larvae from Queensland (Gatton) and South Australia (Waite) were collected and reared on the cabbage plant at the University of Queensland in Australia. Total RNA was extracted from fifteen 3rd instar larval samples using Triazol® following the manufacturerâs protocol (Life Technologies). The small RNA libraries were generated from both populations with three biological replicates using the Illumina Truseq small RNA preparation kit at the Australian Genome Research Facility (AGRF-Melbourne, Australia). The purified cDNA libraries were sequenced on Illumina HiSeq and raw sequencing reads (50 nt) were obtained using Illuminaâs Sequencing Control Studio software.
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