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ABSTRACT: Illumina RNA-Seq of tea

PROVIDER: PRJNA524304 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8632517_1.fastq.gz	Fastqsanger.gz
	SRR8632517_2.fastq.gz	Fastqsanger.gz
	SRR8632518_1.fastq.gz	Fastqsanger.gz
	SRR8632518_2.fastq.gz	Fastqsanger.gz

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Transcriptional response of tea roots of different genotypes to potassium

Project description:Purpose: We investigated root foraging strategies for K of tea plants using a multi-layer split-root system by RNA-seq. Methods: One-year old tea cuttings were cultivated with the roots evenly planted on the two sides of the split root hydroponic box with a root canal. Three treatments were included to simulate the heterogeneous and homogeneous K environments. After 5d treatment, the roots on the two sides of the split root hydroponic box were collected separately and the RNA sequencing were analyzed by the Illumina Hiseq (2500, Illumina, San Diego, CA). Results: RNA-seq data had a linear relationship with qRT–PCR (r2=0.76), which confirmed the reliability of the RNA-seq data. Conclusions: Our study screened the key genes of tea root system to adapt to potassium heterogeneity.

2022-08-17 | GSE198198 | GEO

Development of a 44K custom oligo microarray using 454 pyrosequencing data for large scale gene expression analysis in tea plant (Camellia sinensis)

Project description:To investigate the large-scale gene expression in different tea clones, a custom oligo microarray was developed using sequences from RNA-seq for probe designing. We succeeded in developing a tea oligo microarray resource which can be successfully used to analyze gene expression in any tea clones without the need for prior sequence knowlege.

2015-01-01 | GSE52255 | GEO

Elucidation of the epitranscriptomic RNA modification landscape of chikungunya virus

Project description:<p>The genomes of positive-sense (+) single-stranded RNA (ssRNA) viruses are believed to be subjected to a wide range of RNA modifications. In this study, we focused on the chikungunya virus (CHIKV) as a model (+) ssRNA virus to study the landscape of viral RNA modification in infected human cells. Among the 32 distinct RNA modifications analyzed by mass spectrometry, inosine was found enriched in the genomic CHIKV RNA. However, orthogonal validation by Illumina RNA-seq analyses did not identify any inosine modification along the CHIKV RNA genome. Moreover, CHIKV infection did not alter the expression of ADAR1 isoforms, the enzymes that catalyze the adenosine to inosine conversion. Together, this study highlights the importance of a multidisciplinary approach to assess the presence of RNA</p><p>modifications in viral RNA genomes.</p>

2024-06-11 | MTBLS8697 | MetaboLights

Project description:RNA-Seq for Tea

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Expression profiling changes during different albescent stages of 'Anji Baicha' (Camellia sinensis)

Project description:The RNA-Seq was used to analyze the expression profiling of genes in different ablescent stages of 'Anji Baicha' Examination of three tea leaf samples in yellow stage, white stage and green stage

2016-09-01 | E-GEOD-66615 | biostudies-arrayexpress

Genome-wide identification of microRNAs responsive to Ectropis oblique feeding in the tea plant (Camellia sinensis L.)

Project description:micro RNA identification of tea plant

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Project description:RNA-Seq of tea leaves

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TEAD1 condensates are transcriptionally inactive storage sites on the pericentromeric heterochromatin

Project description:TEA domain transcription factor 1 (TEAD1), a Hippo pathway transcription factor important in cellular homeostasis and development, is increasingly implicated in cancer biology. Here, we reveal a novel role for TEAD1 in organizing nuclear condensates, independent of active transcription. Using high-resolution imaging, ChIP-seq, RNA-seq and proximity-based proteomics, we demonstrate that in patient-derived renal cell carcinoma cells, TEAD1 forms micron-sized foci by binding to the heterochromatic pericentromeric regions using its DNA-binding domain. These TEAD1 foci do not mediate transcription but instead serve as depots for excess TEAD1. This contrasts with TEAD1 organization in other genomic regions of both RCC and normal kidney cells, where TEAD1 associates with markers of active transcription. Our findings provide a mechanistic framework for TEAD1’s dual regulatory roles, offering new insights into its contribution to transcriptional dysregulation and tumor progression.

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Transcriptome analysis of Botrytis cinerea in response to tea tree oil and its two characteristic components

Project description:Purpose: High-throughput RNA sequencing has been used to examine mRNA expression profiles in fungal cells treated with essential oils. The goals of this study are to analyze the global gene expression profiles in Botrytis cinerea with or without tea tree oil and its two characteristic components treatment by RNA-Seq. Methods: The mRNA profiles of Botrytis cinerea with or without tea tree oil and its two characteristic components treatment were generated by deep sequencing, in triplicate, using Illumina HiSeq™ 2500 sequencing platform. 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. qRT–PCR was performed to verified the sensitivity of the RNA-seq method. Results: After high-throughput RNA sequencing, reads were filtered to yield 111.22 Gb of clean sequence data. The GC content for all samples exceeded 45%. The Q20 ratio (used to evaluate reads quality) was greater than 94%, and Q30 base percentage was at least 87.07%. Altered expression of 7 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Most differentially expressed genes (DEGs) from B. cinera cells treated with terpinen-4-ol participated in biosynthesis of secondary metabolites, and the metabolism of amino acid, carbohydrate and lipid. 1,8-cineole mainly affected DEGs involved in genetic information processing, and thus inducing cell death. Conclusions: Terpinen-4-ol exerts antifungal activity mainly by blocking the expression of genes related to cell integrity and mitochondrial function. 1,8-cineole primarily affects genes involved in genetic information processing including DNA replication, transcription and repair. This study provides insight into the molecular mechanism by which tea tree oil acts against Botrytis cinerea based on the data from RNA-seq.

2019-10-03 | GSE138291 | GEO

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