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Next Generation Sequencing Facilitates Quantitative Analysis of in 14-day-old wt and val1 val2 pkl seedlings.

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of in 14-day-old wt and val1 val2 pkl seedlings.

PROVIDER: PRJNA772750 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16490690_1.fastq.gz	Fastqsanger.gz
	SRR16490690_2.fastq.gz	Fastqsanger.gz
	SRR16490691_1.fastq.gz	Fastqsanger.gz
	SRR16490691_2.fastq.gz	Fastqsanger.gz
	SRR16490692_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of in 14-day-old wt and val1 val2 pkl seedlings.

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: RNA from 14-day-old seedlings of wild-type and pkl was isolated using the RNAprep Pure Plant Kit as described above. RNAs from three biological replicates was sequenced separately at Novogene, using Illumina Hiseq X-Ten (Sequencing method: Hiseq-PE150). Results: Reads were mapped to the TAIR10 Arabidopsis genome using TopHat (Galaxy V2.1.1 in usegalaxy.org) with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 5,000 bp were required (Paired-end). Then, mapped reads were assembled according to TAIR10 version of genome annotation using cufflinks (version 2.1.1) with default settings. To analyze differential expression, the assembled transcripts from three independent biological replicates in Col and other mutants were included and compared using Cuffdiff (version 2.1.1) with default settings. 14-day-old seedling of WT and val1 val2 pkl were performed RNA-seq to analyzed their differential expression genes in Arabidopsis.

2022-12-12 | GSE186156 | GEO

Identify differentially expressed genes in 14-day-old pkl seedlings

Project description:CHD3 proteins are ATP-dependent chromatin remodeling factors that are components of diverse multisubunit complexes that can either repress or activate gene expression. In plants, the CHD3 protein PICKLE (PKL) is necessary for repression of seed-specific genes during germination and promotes deposition of the repressive epigenetic mark trimethylation of histone H3 lysine 27 (H3K27me3). It is unknown, however, if PKL acts directly at H3K27me3-enriched loci. We undertook a microarray analysis of 14-day-old plants and found that PKL continues to play an important role in expression of H3K27me3-enriched genes and in specification of developmental identity after germination. We used microarray to identify genes that are differentialy expressed in 14-day-old pkl seedlings and used chormatin immunoprecipitation to identify genes that are the direct targets of PKL. Wild-type (Col-0) and pkl-1 seedlings were grown on 1/2 MS plates with constant light and harvsted after 14-day growth. Three biological replicates.

2012-01-01 | E-GEOD-31639 | biostudies-arrayexpress

Identify differentially expressed genes in 14-day-old pkl seedlings

2012-01-01 | GSE31639 | GEO

VAL1/2 recruit PKL to target sites in arabidopsis genome

Project description:PICKLE (PKL), a Chromodomain Helicase DNA binding domain type 3-type (CHD3) chromatin remodeler, noted for an embryonic structure called pickle root in primary root tip in pkl mutant, has been studied for decades. we obtained a comprehensive genome occupancy of PKL by Chromatin immunoprecipitation-sequencing (ChIP-seq), and found PKL co-occupy with the major repressors of seed maturation program, VIVIPAROUS1/ABI3-LIKE1/2 (VAL1/2) in genome. Furthermore, PKL physically interacts with VAL1/2 in vivo and phenotype and transcriptome data indicated that PKL and VAL1/2 function in a common pathway. Moreover, ChIP-seq and ChIP-qPCR results showed that VAL1/2 are necessary for the recruitment of PKL to co-target genes

2023-05-10 | GSE186157 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of in 14-day-old wt and pkl seedlings.

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: RNA from 14-day-old seedlings of wild-type and pkl was isolated using the RNAprep Pure Plant Kit as described above. RNAs from three biological replicates was sequenced separately at Novogene, using Illumina Hiseq X-Ten (Sequencing method: Hiseq-PE150). Results: Reads were mapped to the TAIR10 Arabidopsis genome using TopHat (Galaxy V2.1.1 in usegalaxy.org) with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 5,000 bp were required (Paired-end). Then, mapped reads were assembled according to TAIR10 version of genome annotation using cufflinks (version 2.1.1) with default settings. To analyze differential expression, the assembled transcripts from three independent biological replicates in Col and other mutants were included and compared using Cuffdiff (version 2.1.1) with default settings. 14-day-old seedling of WT and pkl were performed RNA-seq to analyzed their differential expression genes in Arabidopsis.

2022-12-12 | GSE186152 | GEO

RNA-seq of WT, val1, val2, and val1 val2 14-day-old seedling in Arabidopsis

Project description:14-day-old seedling of WT, val1, val2, and val1val2 were performed RNA-seq to analyzed their differential expression genes in Arabidopsis.

2020-11-06 | GSE119715 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of in 14-day-old wt and pkl seedlings.

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of in 14-day-old wt and pkl seedlings.

| PRJNA772746 | ENA

RNA-seq of WT, val1, val2, and val1 val2 14-day-old seedling in Arabidopsis

Project description:RNA-seq of WT, val1, val2, and val1 val2 14-day-old seedling in Arabidopsis

| PRJNA490100 | ENA

VAL1/2 recruit PKL to target sites in arabidopsis genome

Project description:VAL1/2 recruit PKL to target sites in arabidopsis genome

| PRJNA772752 | ENA

Transcriptomics analysis of developing wild type and val1 mutant Arabidopsis embryos

Project description:Developing Arabidopsis seeds accumulate oils and seed storage proteins synthesized by the pathways of primary metabolism. Seed development and metabolism are positively regulated by transcription factors belonging to the LAFL regulatory network. The VAL gene family encodes repressors of the seed maturation program in germinating seeds, although they are also expressed during seed maturation. VAL1 functions as a repressor of seed metabolism, as val1 mutant seeds accumulated elevated levels of storage proteins compared to the wild type. Two VAL1 splice variants were identified through RNA sequencing analysis: a full-length and a truncated form lacking the plant-homeodomain-like domain associated with epigenetic repression. None of the transcripts encoding the core LAFL network transcription factors were affected in val1 embryos. Instead, activation of VAL1 by FUSCA3 appears to result in repression of a subset of seed maturation genes downstream of core LAFL regulators as 39% of transcripts in the FUSCA3 regulon were de-repressed in the val1 mutant. The LEC1 and LEC2 regulons also responded but to a lesser extent. Additional 832 transcripts that were not LAFL targets were de-repressed in val1 mutant embryos. These transcripts are candidate targets of VAL1, acting through epigenetic and/or transcriptional repression. 2 genotypes, 7 time points, 3 biological and 4 technical replicates

2016-02-19 | E-GEOD-74692 | biostudies-arrayexpress

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