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Next Generation Sequencing to Study LUX-affected genes.

ABSTRACT: Next Generation Sequencing to Study LUX-affected genes.

PROVIDER: PRJNA475754 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7295310.fastq.gz	Fastqsanger.gz
	SRR7295320.fastq.gz	Fastqsanger.gz
	SRR7295330.fastq.gz	Fastqsanger.gz
	SRR7295340.fastq.gz	Fastqsanger.gz
	SRR7295311.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing to Study LUX-affected genes.

Project description:Purpose: The goals of this study are to compare RNA-seq profiles of Col-0, acd6-1, Iux-1, and acd6-1lux-1 to identify genes affected by LUX. Methods: Total RNA was extracted from 25-d old Col-0, lux-1, acd6-1, or acd6-1lux-1 plants collected at ZT1 or ZT13. Triplicate biological samples were used for most genotypes at each time point, except acd6-1 and acd6-1lux-1 at ZT13, which had duplicate samples. 0.5 ug RNA per replicate was used to generate cDNA libraries using Illumina TruSeq RNA sample preparation kit (catalog no. RS-122-2001). The samples were multiplexed and sequenced using the Illumina HiSeq sequencing platform in Genomics Resources Core Facility at Weill Cornell Medical College. Sequencing was conducted with a standard run of 51 cycles and single reads. At least 150 million reads per lane were obtained for sequencing. qRT–PCR validation was performed using TaqMan and SYBR Green assays for some selected genes. Results: We found that over 1500 genes are affected by lux-1 based on the RNAseq analysis. GO analysis revealed that LUX-affected genes are enchriched in response to abiotic and biotic stimuli. In particular, genes involved in basal defense, salicyclic acid signaling, and jasmonic acid signaling are affected by lux-1. We also found LUX regulation of the clock genes, including core clock components and those acting in the output pathways. Conclusions: The RNAseq analysis support a role of LUX in regulation of the circadian clock and plant defense.

2019-06-12 | GSE115680 | GEO

Next Generation Sequencing to Study FLK-affected genes

Project description:Next Generation Sequencing to Study FLK-affected genes

| PRJNA690591 | ENA

Next Generation Sequencing to Study FLK-affected genes

Project description:Purpose: The goals of this study are to compare RNA-seq profiles of Col-0, acd6-1, flk-1, flk-5, acd6-1flk-1, and acd6-1flk-5 to identify genes affected by FLK. Methods: Total RNA was extracted from 25-d old plants. A total amount of 1 μg RNA per sample was used to generate cDNA libraries, using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Deep sequencing was performed using Illumina NovaSeq 6000 (Novogene Corporation Inc.). Triplicate biological samples were used for all genotypes except acd6-1flk-5, which had duplicate samples because one sample failed to pass quality control. The samples were multiplexed and sequenced with the standard paired-end sequencing that has a read length of 150bp per end and 20M reads per end per sample. Results: We found that over 8000 genes are differentially affected by FLK based on the RNAseq analysis. GO analysis revealed that FLK-affected genes are enchriched for genes involved in primary metabolism and in response to abiotic and biotic stimuli. Conclusions: The RNAseq analysis support a role of FLK in regulation of plant development and defense.

2023-04-12 | GSE164424 | GEO

Exploring ILF2 regulatory genes by next-generation sequencing

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Next Generation Sequencing facilitates Quantitative Analysis of mouse CD4+ T cells affected by Gpr120

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Next Generation Sequencing identifies differential genes regulated by FTSJ1 overexpression

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Next generation sequence analysis

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Targeted Next-generation Sequencing Panel for Identification of Germline Mutations in Early Onset Cancers With Sporadic or Hereditary Presentation

Project description:Despite relevant clinical and/or familial presentations suggesting a hereditary predisposition (early-onset, multiple primary tumors, familial aggregation), targeted genomic analysis based on the phenotype are often non contributive. As somatic cancer genes are limited, the hypothesis is that the targeted next-generation sequencing of 200 genes, selected for their implications in cancers may contribute to the understanding of many selected patients’ presentation by the identification of germline deleterious mutations, and may identified phenotype overlapping and/or mosaicisms. The focus will be put on early-onset breast, ovarian, colorectal cancer or pediatric cancers and multiple primary tumors.

| 2206884 | ecrin-mdr-crc

Identification of Hepatic Genes Regulated by ATF3 using Next Generation Sequencing

Project description:Identification of Hepatic Genes Regulated by ATF3 using Next Generation Sequencing

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A Next-Generation Sequencing Study in a Cohort of Patients with Parkinson’s Disease

Project description:Background: Parkinson’s disease (PD) is a multisystem and multifactorial disorder. Therefore, the application of modern genetic techniques may assist in unraveling its complex pathophysiology. Methods: We conducted a clinical-demographic evaluation of 126 patients with PD, all of whom were Caucasian and of Sicilian ancestry. DNA was extracted from peripheral blood for each patient, followed by sequencing using a Next-Generation Sequencing system. This system was based on a custom gene panel comprising 162 genes. The sample underwent further filtering, taking into account allele frequencies of genetic variants, their presence in the Human Gene Mutation Database, and their association in the literature with PD or other movement/neurodegenerative disorders. Results: The largest number of variants was identified in the leucine-rich repeat kinase 2 (LRRK2) gene. However, variants in other genes, such as acid beta-glucosidase (GBA), DNA polymerase gamma, catalytic subunit (POLG), and parkin RBR E3 ubiquitin protein ligase (PRKN), were also discovered. Interestingly, some of these variants had not been previously associated with PD. Conclusions: Enhancing our understanding of the genetic basis of PD and identifying new variants possibly linked to the disease will contribute to improved diagnostic accuracy, therapeutic developments, and prognostic insights for affected individuals.

2024-10-14 | E-MTAB-13523 | biostudies-arrayexpress

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