Project description:Genome-wide target genes of PPD2 were identified through ChIP-seq on Arabidopsis cell cultures. For ChIP-seq, PPD2 was fused to the GSyellow TAP tag and expressed from the 35S promoter. The p35S:PPD2-GSyellow construct was transformed into Arabidopsis thaliana PSB-D cell culture. ChIP was performed using anti-GFP antibody (abcam290).
Project description:Whole genome sequencing of the Arabidopsis thaliana dot5-1 transposon insertion line described in Petricka et al 2008 The Plant Journal 56(2): 251-263.
Project description:A PSB-D wild type Arabidopsis thaliana cell culture (Arabidopsis Biological Resource Center stock: CCL84840) was grown after subculturing for one week and divided into separate 10 mL samples for 24 h. Samples were then treated with 50 µM RubNeddin1 (RN1, Chembridge ID 6389186), 2,4-D, or an equal volume of DMSO. Total RNA was extracted from each 10 mL cell culture sample, for each of at least 3 biological replicates, RQ1 RNase-free DNase (Promega) was used for the on-column DNase digestion step. A Trueseq RNA-Seq library (Illumina) was compiled and sequenced as 50-bp single read using Illumina HiSeq 2000. Control samples (3) for this experiment were submitted under accession number E-MTAB-3915
Project description:Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput bisulfite sequencing Whole genome shotgun bisulfite sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.
Project description:We conducted whole-genome bisulfite sequencing (WGBS) of Arabidopsis thaliana mutation accumulation (MA) lines under different temperature treatments over sucessive generations, and then we identified the global methylation in each MA line. Our result showed taht DNA methylation was observed more frequently at DNA mutation sites, indicating its contribution to the mutation process at elevated temperatures.
Project description:Plant Topless-related 1 (TPR1), belonging to a family of transcriptional corepressors found across eukaryotes, contributes to immunity signaling in Arabidopsis thaliana and wild tobacco. We used chromatin immunoprecipitation and sequencing (ChIP-seq) of Arabidopsis TPR1-GFP expressing transgenic lines to characterize genome-wide TPR1-chromatin associations.
Project description:a2e_heterosis - cgh_colvscvi_wg - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - Comparative genome hybridization between Arabidopsis thaliana accessions Col-0 and CVi.
Project description:a2e_heterosis - cgh_colvsc24_wg - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - Comparative genome hybridization between Arabidopsis thaliana accessions Col-0 and C24.
Project description:To identify the genomic binding sites of FRS12, Tandem Chromatin Affinity Purification â Seq (TChAP-Seq) was performed on 7-d-old Pro35S:FRS12-HBH and Pro35S:NLS-GFP-HBH expressing Arabidopsis thaliana PSB-D cells. Cultures were transferred to long days (16:8) conditions two weeks before harvesting at night time (NT) at zeitgeber time (ZT) 20 (time of lights on usually defines zeitgeber time zero). Chromatin was isolated from formaldehyde-treated cell cultures following two affinity purification steps; first by IMAC using a Ni-NTA Superflow resin (Qiagen), then by a Biotin binding step using a Streptavidin Sepharose resin (GE Healthcare). Finally, protein-DNA bound fragments were decrosslinked, deproteinized and purified using QIAquick PCR Purification Kit (Qiagen). Pro35S:FRS12-HBH samples were carried in two replicates whereas background Pro35S:NLS-GFP-HBH sample was prepared in a single replicate. The TChAP DNA samples were processed by first preparing a TruSeq ChIPseq library (Illumina) and then sequenced using Illumina HiSeq 2000 at 50bp single read at an average depth of 15 million reads.