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Next Generation Sequencing Facilitates Quantitative Analysis of in 14-day-old wt, brm-1, brm-3, brip1, brip2, brip1 brip2, brip1 brip2 brm-3 and brip1 brip2 brm-1 seedlings.

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of in 14-day-old wt, brm-1, brm-3, brip1, brip2, brip1 brip2, brip1 brip2 brm-3 and brip1 brip2 brm-1 seedlings.

PROVIDER: PRJNA597766 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10769000_1.fastq.gz	Fastqsanger.gz
	SRR10769000_2.fastq.gz	Fastqsanger.gz
	SRR10769001_1.fastq.gz	Fastqsanger.gz
	SRR10769001_2.fastq.gz	Fastqsanger.gz
	SRR10769002_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of in 14-day-old wt, brm-1, brm-3, brip1, brip2, brip1 brip2, brip1 brip2 brm-3 and brip1 brip2 brm-1 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, brip1, brip2, brm-3, brm-1, brip1 brip2, brip1 brip2 brm-3 and brip1 brip2 brm-1 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 4,000 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. Conclusions: Our study represents the first detailed analysis of brip1, brip2, brip1 brip2 transcriptomes, with biologic replicates, generated by RNA-seq technology.

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Next Generation Sequencing Facilitates Quantitative Analysis of in 14-day-old wt, brm-1, brd1,2,13 and brm-1 brd1,2,13 seedlings

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Genome-wide profiling of SWI/SNF chromatin remodeler BRAHMA (BRM) and BRM Interacting Protein 1/2 (BRIP1/2) in Arabidopsis

Project description:SWI/SNF chromatin remodeling complexes control gene expression by regulating chromatin structure. However, the full subunit composition of SWI/SNF complexes in plants remains unclear. Here we show that BRAHMA Interacting Protein 1 (BRIP1) and BRIP2 in Arabidopsis thaliana are core subunits of plant SWI/SNF complexes. BRIP1 and 2 are two homolog proteins. brip1 brip2 double mutants exhibit developmental phenotypes and a transcriptome strikingly similar to those of BRAHMA (BRM) mutants. Genetic interaction tests indicated that BRIP1 and 2 act together with BRM to regulate gene expression. Furthermore, BRIP1 and 2 physically interact with BRM-containing SWI/SNF complexes, and extensively co-localize with BRM at endogenous genes. Loss-of-brip1brip2 results in decreased BRM occupancy at almost all BRM target genes and substantially reduced subunits incorporation into the BRM-containing SWI/SNF complexes. Together, our work identifies new core subunits of BRM-containing SWI/SNF complexes in plants, and uncovers the essential role of these subunits in regulating the integrity (assembly) of SWI/SNF complexes in plants.

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RNA-seq Analysis of 14-day-old WT, bcl7a(brip3), bcl7b(brip4), bcl7a bcl7b(brip3 brip4), bcl7a bcl7b brm-3(brip3 brip4 brm-3) and bcl7a bcl7b brm-1(brip3 brip4 brm-1) seedlings under short day condition

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Project description:Wide-type, brm, clf, and brm clf mutant seedlings

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