Project description:Drosophila PBAP complex, a form of SWI/SNF class of complexes, played a important role in metamorphosis. We conducted next-generation sequencing (NGS) to analyse the expression profile in both control and Brm knockdown fly larvae.
Project description:Drosophila PBAP complex, a form of SWI/SNF class of complexes, played a important role in metamorphosis. We conducted MNase digestion followed by next-generation sequencing (NGS) to analyse the nucleosome profile in both control and Brm knockdown fly larvae.
Project description:Purpose：Examination of global gene expression 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. Methods: Total RNA was extracted from 14-day-old Arabidopsis seedlings under short-day conditions using TRIzol reagent (Invitrogen) following the manufacturer's instructions. RNAs from three biological replicates was sequenced. separately at Novogene, using Illumina Hiseq X-Ten (Sequencing method: Hiseq-PE150). The paired-end RNA-seq reads were quantified by Salmon(Patro et al., 2017) (v1.5.1) with parameters -k 31 and --type quasi. Salmon index was generated using AtRTD2.fa as the reference transcriptome. The gene quantification files of all samples were used as inputs (TPM values) for differential gene expression analysis by DESeq2(Love et al., 2014) v3.10. To analyze differential gene expression in all samples, we used “parametric” Fit type, “ratio” method for estimate Size Factors and Wald significance test function provided by DESeq2. Conclusions: Our study represents the first detailed analysis of 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) transcriptomes, with biologic replicates, generated by RNA-seq technology.
Project description:By using ChIP-seq, we found that loss of BRM activity in developing seedlings leads to ectopic and increased H3K27me3 deposition at several hundred genes, indicating the critical role of BRM in preventing the inappropriate deposition of this histone mark. Removal of CLF in brm mutant could partcially suppress the increased H3K27me3. Examination of H3K27me3 in 14-day-old wt, brm, clf, and brm clf seedlings. Two biological replicates for each one.
Project description:Arabidopsis brm plants depleted in a SWI/SNF-type ATPase BRM have decreased level of endogenous gibberellins and a phenotype that in many respects resembles the phenotype of mutants with repressed GA signaling or biosynthesis, like ga1-3. ga1-3/brm double mutant showed several additive and synergistic effects. To examine whether the phenotypic traits of brm, ga1-3 and ga1-3/brm lines are reflected at the gene expression level, we compared the expression profiles of brm, ga1-3, ga1-3/brm and wild-type plants using microarray analysis. Microarray analysis was performed on total RNA isolated from shoots of 18-d-old wt, brm, ga1-3, and ga1-3/brm seedlings. Three biological replicates were examined for each genotype. Plants were grown simultaneously under the same conditions.
