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Next Generation Sequencing of Wild Type and AtSRT1 transgene plants Transcriptomes

ABSTRACT: Next Generation Sequencing of Wild Type and AtSRT1 transgene plants Transcriptomes

PROVIDER: PRJNA412814 | ENA |

REPOSITORIES: ENA

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Next Generation Sequencing of Wild Type and AtSRT1 transgene plants Transcriptomes

Project description:To study genome-wide gene expression regulated by AtSRT1, we analyzed transcriptomes of wild type and AtSRT1 RNAi-1 (R) and overexpression OX-SRT1-1(OX) line by RNA-sequencing using the Illumina Hiseq-2000 sequencing system. Three biological replicates for each genotype were tested.The data suggest that AtSRT1 plays an important role in regulation of genes involved in stress responses and in carbon and energy metabolism in Arabidopsis.

2018-04-01 | GSE104483 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and OsAFB6 overexpression mutant Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transgene-derived OsAFB6 overexpression mutant transcriptome profiling (RNA-seq) to microarray Methods: young panicle(<1mm) mRNA profiles of 80 individual plants of OsAFB6 overexpression mutants and the correspondinng negative plants during the same transgenic event as control were generated by deep sequencing, in two replicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we found 59 genes were upregulated and 229 genes were down regulated in OsAFB6 overexpression mutant. Conclusions: Our study represents the first detailed analysis of young panicle transcriptomes of OsAFB6 overexpression mutant, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2017-11-16 | GSE106954 | GEO

Next generation sequencing analysis of Colletotrichum camelliae transcriptomes in response to tea plants.

Project description:Next generation sequencing was performed to identify genes changed in Colletotrichum camelllae upon infection tea plants. The goal of the work is to find interesting genes involved in fungal virulence. The object is to reveal the molecular mechanism of funal virulence.

2023-01-25 | GSE205689 | GEO

Next Generation Sequencing Facillitates Quantitative Analysis of Wild Type and snrk1a1/a2 mutant Transcriptomes

Project description:Next Generation Sequencing Facillitates Quantitative Analysis of Wild Type and snrk1a1/a2 mutant Transcriptomes

2021-12-31 | GSE183118 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of ZH11 and nf-yc11 mutant plants Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of ZH11 and nf-yc11 mutant plants Transcriptomes

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Next Generation Sequencing Facilitates Quantitative Analysis of ZH11 and ONAC127/ONAC129 transgenic plants Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of ZH11 and ONAC127/ONAC129 transgenic plants Transcriptomes

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Next Generation Sequencing of Wild Type and Oslec1-1 Transcriptomes

Project description:Next Generation Sequencing of Wild Type and Oslec1-1 Transcriptomes

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Epigenetic differences between transgenes and endogenous genes promote transgene silencing in plants

Project description:Transgene loci that spontaneously undergo RNA silencing have been instrumental to decipher RNA silencing pathways in plants. In contrast, transgene loci that are stably expressed have been poorly characterized. Here we show that stably expressed transgene loci epigenetically differ from endogenous genes. Impairing the histone H3K4me3 demethylase JMJ14 increases DNA methylation at stably expressed transgene loci but not at endogenous genes, whereas impairing the histone H3K9me2 demethylase IBM1 increases DNA methylation at endogenous genes, but decreases DNA methylation at stably expressed transgene loci. Moreover, impairing IBM1 promotes post-transcriptional gene silencing (PTGS) at stably expressed transgene loci, whereas impairing JMJ14 prevents PTGS induced systemically by grafting onto silenced rootstocks. Given that impairing DNA methylation suppresses the effect of impairing JMJ14 and restores transgene capacity to undergo graft-induced PTGS, we propose that transgene DNA methylation prevents PTGS, likely by limiting the transcription of aberrant RNA by-products that are transformed into dsRNA by cellular RNA-dependent RNA polymerases to activate PTGS.

2021-03-25 | GSE152584 | GEO

Bisulfite (methylome) sequencing of msh1 memory line and non-memory (normal looking) sibling plants with isogenic Col-0 wild-type control in Arabidopsis [generation 2 to 6]

Project description:Col-0 plants were transformed with MSH1 RNAi construct. Transgene positive plant was self pollinated and transgene was segregated in subsequent generation, and screened for presence of transgene using PCR assay. Of transgene null plants, 20% plants displayed delayed in flowering, smaller in size, and lighter green termed as memory phenotype. Memory plants were self pollinated for six generations and plants from each generations were Bisulfite sequenced.

2020-04-03 | GSE129303 | GEO

Next Generation Sequencing Analysis of Wild Type and fl3 Transcriptomes in 10DAP(day after pollination) endosperm

Project description:Maize floury3 (fl3) is a classic semi-dominant mutant that shows severe defects in the endosperm but appears normal in the plant.The goals of this study are to compare WT to fl3 transcriptomes in 10DAP(day after pollination) endosperm by Next Generation Sequencing.

2017-07-22 | GSE95039 | GEO

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