Ontology highlight
ABSTRACT:
PROVIDER: PRJNA769837 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16268613.fastq.gz | Fastqsanger.gz | |||
| SRR16268614.fastq.gz | Fastqsanger.gz | |||
| SRR16268615.fastq.gz | Fastqsanger.gz | |||
| SRR16268616.fastq.gz | Fastqsanger.gz | |||
| SRR16268617.fastq.gz | Fastqsanger.gz |
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Project description:Next-generation sequencing (NGS) was used to analysis the expression profiling of cotton seedlings under TOR inhibition by AZD. TOR inhibition significantly altered the expression levels of anabolic and catabolic processes related genes, photosynthesis and phytohormone signaling pathways related genes. Expression profiling analysis reveals that TOR is a key player in cotton seedlings growth.
2017-03-08 | GSE95767 | GEO
Project description:Purpose: Identification and characterization of thermotolerance candidate genes during early seedling stage by comparative transcriptome analysis. We performed transcriptome sequencing (mRNA-seq) of cotton leaves under high temprature stress using Illumina sequencing technology. And quantitative reverse transcription polymerase chain reaction (qRTâPCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: A comparative transcriptomics approach was used to monitor gene differential expression at two time points (4 and 8 h) in leaves of the two cotton genotypes under high temprature conditions. Results: During a 8-h salt exposure,among 9,777 differentially expressed unigenes (DEUs) were identified during at least one time point, 7,296 DEUs representing different classes of protein kinases, transcription factors, and heat shock proteins as well as downstream thermotolerance-related genes are reported. Gene ontology enrichment and biochemical pathway analyses showed these DEUs were mainly related to carbohydrate metabolism, secondary metabolites, and plant hormone signalling. Conclusions: Our findings offer high efficiency technique for early charactering thermotolerance in cotton and provide the information for the candidate genes to improve thermotolerance of cotton cultivars. Leaf mRNA profiles of 20-day-old seedlings of two cotton genotypes, one heat tolerant and the other heat sensitive during a 8-h high-temperature exposure were generated by deep sequencing, using Illumina HiSeq 2000 system.
2016-06-30 | E-GEOD-70205 | biostudies-arrayexpress
Project description:Hpa1Xoo-Mediated Transcriptome in Transgenic Cotton Reveals the Constitutively Expressed Diverse Defense genes in Multiple Signaling Pathways Associated with Hypersensitive Cell Death Like other harpins, harpinXoo enables plants to acquire multiple resistance to pathogen and insect attack. However, the molecular model is not fully understood, especially in transgenic plant harpinXoo for genome-wide constitutive expression. Here, we showed that 530 cDNAs differentially expressed in transgenic hpa1Xoo-harboring cotton (T-34) compared to its receiptor (Z35), through analyzing the transcriptome profile in a customized cotton 12k cDNA microarray, which was enriched in 34 pathways. Among them, 123 genes were identified from T-34 as hypersensitive reaction-mediated defense genes, involved in reactive oxygen species-, salicylic acid-, jasmonates-, ethylene-, auxin-, abscisic acid-, and Ca2+-mediated signaling pathways, and we uncovered various components of defense responses associated with recognition of the pathogen-derived elicitor. Apart from elevated genes for basic defense, harpinXoo activated leucine-rich-repeat plant receptor kinases and mitogen-activated protein kinase cascade to strengthen downstream defense responses, including production of antimicrobial compounds in T-34. Defense genes from T-34 were expressed at a much higher level in response to pathogen infection compared with Z35. Simultaneous up- and down-regulation in differentially-expressed genes, and increased expression of genes encoding energy producing and consuming pathways, suggested that energy balance was maintained in the genetically modified cotton without biotic stress. High-energy demand only occurred following pathogen infection. Using kanamycin-resistance tests, positive plants were successfully screened from transgenic cotton T-34 T6 progenies; all the receiptor Z35 plants gave negative results. We randomly selected three positive plants for polymerase chain reaction (PCR) analysis; the different positive bands (420, 310 and 180 bp) were confirmed as harpinXoo, the 35s promoter, and the NOS terminator, respectively, by sequencing and BLAST searches (www.ncbi.nlm.nih.gov.). For further analysis, the positive results were confirmed by Southern and western blots. Three positive bands were obtained in each T-34 sample located at about 4, 6 and 10 kb in the Southern blot. This pattern suggests that T-34 incorporated the harpinXoo transgene at multiple chromosomal locations. Western blot analysis showed that the harpinXoo protein was constitutively expressed in T-34 transgenic lines, whereas it was barely detectable in Z35 (data not shown). The transgenic plants contained a selectable ‘marker’ gene, neomycin phosphotransferase II (nptII). Previous research showed that expression of marker genes (e.g. nptII, uidA, hph and uidA-gfp) did not contribute to visible phenotypes in transgenic plants. The non-targeted transgenic and non-transgenic plants were equivalent in their global patterns of transcription (El Ouakfaoui and Miki, 2005). Thus, the present study examined the many differences between T-34 and its receiptor Z35 in regard to the whole genome expression of G. hirsutum using microarrays to monitor changes in individual gene expression level effected by harpinXoo. All experiments were conducted using the 12k cotton cDNA microarray, and cotton true leaves and roots at the 4–5-true-leaf-stage. The use of this microarray enabled a quantitative approach to examine changes in transcript level for all genes within the G. hirsutum genome; as a result, inferences can be drawn regarding the molecular effects of transgenic cotton expressing harpinXoo. There were three biological replicates in the experiment for each organ.
2010-12-01 | E-GEOD-20446 | biostudies-arrayexpress
Project description:Hpa1Xoo-Mediated Transcriptome in Transgenic Cotton Reveals the Constitutively Expressed Diverse Defense genes in Multiple Signaling Pathways Associated with Hypersensitive Cell Death Like other harpins, harpinXoo enables plants to acquire multiple resistance to pathogen and insect attack. However, the molecular model is not fully understood, especially in transgenic plant harpinXoo for genome-wide constitutive expression. Here, we showed that 530 cDNAs differentially expressed in transgenic hpa1Xoo-harboring cotton (T-34) compared to its receiptor (Z35), through analyzing the transcriptome profile in a customized cotton 12k cDNA microarray, which was enriched in 34 pathways. Among them, 123 genes were identified from T-34 as hypersensitive reaction-mediated defense genes, involved in reactive oxygen species-, salicylic acid-, jasmonates-, ethylene-, auxin-, abscisic acid-, and Ca2+-mediated signaling pathways, and we uncovered various components of defense responses associated with recognition of the pathogen-derived elicitor. Apart from elevated genes for basic defense, harpinXoo activated leucine-rich-repeat plant receptor kinases and mitogen-activated protein kinase cascade to strengthen downstream defense responses, including production of antimicrobial compounds in T-34. Defense genes from T-34 were expressed at a much higher level in response to pathogen infection compared with Z35. Simultaneous up- and down-regulation in differentially-expressed genes, and increased expression of genes encoding energy producing and consuming pathways, suggested that energy balance was maintained in the genetically modified cotton without biotic stress. High-energy demand only occurred following pathogen infection.
2010-12-01 | GSE20446 | GEO
Project description:We used a next-generation sequencing approach, Illumina Digital Gene Expression (DGE) technology, to Genome-wide profiling of gene expression during cotton SE. As a result, 5,076 differentially expressed genes were identified during cotton SE. Expression profile and functional assignments of these genes indicated significant transcriptional complexity during this process. Transcription factor-encoding genes were found to be differentially regulated during SE. The complex pathways of auxin abundance, transport and response with differentially regulated genes revealed that the auxin-related transcripts belonged to IAA biosynthesis, indole-3-butyric acid (IBA) metabolism, IAA conjugate metabolism, auxin transport, auxin-responsive protein / indoleacetic acid-induced protein (Aux/IAA), auxin response factor (ARF), small auxin-up RNA (SAUR), Aux/IAA degradation, and other auxin-related proteins, which allow an intricate system of auxin utilization to achieve multiple purposes in SE. Quantitative real-time PCR (qRT-PCR) was performed on selected genes with different expression patterns and functional assignments were made to demonstrate the utility of RNA-Seq for gene expression profiles during cotton SE. We report here the first comprehensive analysis of transcriptome dynamics that may serve as a gene expression profile blueprint in cotton SE. Our main goal was to adapt the RNA-Seq technology to this notable development process and to analyse the gene expression profile. Complex auxin signalling pathway and transcription regulation were highlighted. Together with biochemical and histological approaches, this study provides comprehensive gene expression data sets for cotton SE that serve as an important platform resource for further functional studies in plant embryogenesis. differential gene expression analysis at 9 time-points/stages during somatic embryogenesis in cotton by deep sequencing, using Illumina GAIIx.
2012-05-31 | E-GEOD-38209 | biostudies-arrayexpress
Project description:In cotton, after the Bt introduction, lepidopteron pest attack been reduced to a greater extent, however, the sucking pests became major problem. Among the sucking pests, the leafhopper Amrasca biguttula biguttula (Ishida), considered to be a severe pest. Here, we reported the label-free quantitative proteomics to identify putative differentially expressed proteins contributing to leafhopper resistance. The results obtained from this work not only aimed to provide a new clue that will facilitate better understanding of molecular interaction between cotton plant and leafhopper, but also explored the key genes for the development of functional markers in cotton towards leafhopper resistance.
2024-08-29 | PXD038644 | Pride