Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-seq of IDS1-myc using Oryza sativa seedlings

ABSTRACT: IDS1 is a rice AP2-type transcription factor with transcritpional repression activity. To understand how IDS1 regulate rice salt tolerance, the ChIP-seq experiments were performed to identify IDS1 binding site in globle genomic level. The two-weeks-old rice seedlings were lysated and sonificated and IDS1-DNA complexes were immune precipated with myc-antibody and protein A beads. The purified DNA samples were used to construct sequencing libraries and sequenced with Illumina. The data were then analyzed with bio-informatic tools.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Xiliu Cheng

PROVIDER: E-MTAB-6504 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ChIP-seq of WT(with 35S-SUC2 transgene) and proMBD7::gMBD7:4xMYC transgenic plants

Project description:In eukaryotes, heterochromatin is characterized by numerous epigenetic marks, including DNA methylation. Spreading of these marks into nearby active genes must be avoided in order to maintain appropriate gene expression. Here, we uncover Arabidopsis Methyl-CpG-Binding Domain 7 (MBD7) and Increased DNA Methylation 3 (IDM3) as anti-silencing factors that prevent transgene repression and genome-wide DNA hypermethylation. MBD7 preferentially binds to highly methylated, CG-dense regions associated with non-CG methylation and physically associates with other anti-silencing factors, including the histone acetyltransferase IDM1, IDM2, and IDM3. IDM1 and IDM2 were previously shown to facilitate active DNA demethylation by the 5-methylcytosine DNA glycosylase/lyase ROS1. Thus, MBD7 tethers the IDM proteins to methylated DNA, which enables the function of DNA demethylases that in turn establish chromatin boundaries and limit DNA methylation Using ChIP-seq to study the genomic targeting principle of MBD7 protein Examination of MBD7 protein binding principle using ChIP-Seq. WT and proMBD7::gMBD7::4xMYC transgenic plants were used for ChIP-seq.

2015-01-29 | E-GEOD-58789 | biostudies-arrayexpress

Validation of Nri1/Nri2 physical interaction with the Candida albicans RSC complex

Project description:Regulation of gene expression programs is crucial for the survival of microbial pathogens in host environments and for their ability to cause disease. In this study, we investigated the epigenetic regulator RSC (Remodels the Structure of Chromatin) in the most prevalent human fungal pathogen Candida albicans (CaRSC). To precisely determine the composition of the CaRSC complex, we immunopurified Myc-tagged Sth1, the core catalytic subunit of the CaRSC complex encoded by C3_02490C and identified its physical interactors using high-resolution tandem mass spectrometry (LC-MS/MS). Strikingly, we identified two novel hitherto uncharacterized proteins that co-purified with Sth1, C2_01370p (Nri1) and C1_01800p (Nri2), whose homologs are annotated only in the CTG clade of fungi. Here, we performed reciprocal co-immunoprecipitations of Myc-tagged Nri1 and Nri2 followed by LC-MS/MS to validate these interactions. For each condition, biological duplicates were analyzed.

2020-11-11 | PXD017987 | Pride

The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis

Project description:Uridylation is a widespread modification destabilizing eukaryotic mRNAs. Yet, molecular mechanisms underlying TUTase-mediated mRNA degradation remain mostly unresolved. Here, we report that the Arabidopsis TUTase URT1 participates in a molecular network connecting several translational repressors/decapping activators. URT1 directly interacts with DECAPPING 5 (DCP5), the Arabidopsis ortholog of human LSM14 and yeast Scd6, and this interaction connects URT1 to additional decay factors like DDX6/Dhh1-like RNA helicases. Nanopore direct RNA sequencing reveals a global role of URT1 in shaping poly(A) tail length, notably by preventing the accumulation of excessively deadenylated mRNAs. Based on in vitro and in planta data, we propose a model that explains how URT1 could reduce the accumulation of oligo(A)-tailed mRNAs both by favoring their degradation and because 3’ terminal uridines intrinsically hinder deadenylation. Importantly, preventing the accumulation of excessively deadenylated mRNAs avoids the biogenesis of illegitimate siRNAs that silence endogenous mRNAs and perturb Arabidopsis growth and development.

2020-12-01 | PXD022676 | Pride

Targeted inhibition of human breast cancer cell lines selected as model systems of ERBB2-positive/EGFR high breast cancer [RPPA-Longterm]

Project description:EGFR-inhibition is required for targeted therapies of EGFR high/ERBB2 positive breast cancer. Approximately 30% of human ERBB2 positive breast tumors also express EGFR. Three therapeutics were analyzed in five combinations plus control. Each experiment was performed in three biological replicates. This resulted in 180 samples. A dilution series of control lysated was included as control.

2012-10-22 | E-GEOD-36325 | biostudies-arrayexpress

Regulation of histone methylation and gene expression reprogramming in rice inflorescence meristem

Project description:Rice inflorescence meristem (IM) development is critical for panicle size and grain production. The transition from SAM to IM is an important development stage in rice. Here we report the application of ChIP-seq technology for profiling of H3K4me3 and H3K27me3 modification in SAM, IM, SDG711 RNAi IM and jmj703 IM which affect panicle size, respectively, and besides, RNA-seq technology for detecting gene expression diversity betwwen SAM, IM and SDG711 RNAi IM. We found that genome-wide H3K27me3 modification vary between SAM and IM, and thouands of genes lost H3K27me3 in SDG711 and jmj703. Also, we found H3K27me3/H3K4me3 ratio was an important factor for the differential expression of many genes during the transition. Differential expressed genes were found between SAM and IM, 711RNAi and WT, repectively. Many important genes involved in IM activity were repressed by SDG711-mediated H3K27me3 and some of which’s expressions were mis-regulated in SDG711 RNAi. Genome-wide mapping of two histone modifications (H3K4me3 and H3K27me3) in SAM, IM, SDG711 RNAi IM and jmj703 IM, and mRNA transcripts in SAM, IM, SDG711 RNAi IM.

2015-05-14 | E-GEOD-68299 | biostudies-arrayexpress

Unravelling the proteomic profile of rice meiocytes during early meiosis

Project description:Transfer of genetic traits from wild or related species into cultivated rice is nowadays an important aim in rice breeding. Breeders use genetic crosses to introduce desirable genes from exotic germplasms into cultivated rice varieties. However, in many hybrids there is only a low level of pairing (if existing) and recombination at early meiosis between cultivated rice and wild relative chromosomes. With the objective of getting deeper into the knowledge of the proteins involved in early meiosis, when chromosomes associate correctly in pairs and recombine, the proteome of isolated rice meiocytes has been characterized by nLC-MS/MS at every stage of early meiosis (prophase I). Up to 1316 different proteins have been identified in rice isolated meiocytes in early meiosis, being 422 exclusively identified in early prophase I (leptotene, zygotene or pachytene). The classification of proteins in functional groups showed that 167 were related to chromatin structure and remodelling, nucleic acid binding, cell-cycle regulation and cytoskeleton. Moreover, the putative roles of sixteen proteins which have not been previously associated to meiosis or were not identified in rice before, are also discussed namely: seven proteins involved in chromosome structure and remodeling, five regulatory proteins (such as SKP1 (OSK), a putative CDK2 like efector), a protein with RNA recognition motifs, a neddylation-related protein, and two microtubule-related proteins. Revealing the proteins involved in early meiotic processes could provide a valuable tool kit to manipulate chromosome associations during meiosis in rice breeding programs.

2014-08-13 | PXD001058 | Pride

Expression data from infected (Xanthomonas oryzae pv. Oryzae (P10)) leaf in japonica rice (cv. Y73)

Project description:Previously, we successfully introduce the bacterial blight resistance trait from Oryza meyeriana into O. sativa using asymmetric somatic hybridization with O. meyeriana as the donor species. After years of breeding, a progeny named Y73 was generated with recurrent parent O. sativa L. ssp. japonica cv. Dalixiang, and it shows high resistance to broad-spectrum of bacterial blight pathogens Xanthomonas oryzae pv. Oryzae (Xoo). However, the resistance mechanism of Y73 is remain undiscovered. To provide insights into the high resistance phenotype of these plants, we examined the transcriptome response in leaves of Y73 to the bacterial blight infection in this study. Xoo inoculated and mock inoculated rice plants were grown in growth room and the global analysis of gene expression events in rice leaves at 24 hours post inoculation (hpi) were analyzed using Affymetrix Rice GeneChip microarrays. We used microarrays to detail the global programme of gene expression underlying Xoo infection in rice Y73. To find out pathways and genes involved in its high and board-spectrum resistance, microanalysis were carried out on Y73 after Xoo infection at 24 hours post inoculation (hpi). Three independant replicates were perfomed for each treatments.

2012-02-27 | E-GEOD-36093 | biostudies-arrayexpress

Targeted inhibition of human breast cancer cell lines selected as model systems of ERBB2-positive/EGFR high breast cancer [RPPA-HCC1954]

Project description:EGFR-inhibition is required for targeted therapies of ERBB2-positive/EGFR high breast cancer. Approximately 30% of human ERBB2-positive breast tumors also express EGFR. Three targeted therapeutics (erlotinib, pertuzumab, trastuzumab) and two ligands (EGF, HRG) were analyzed in all possible combinations. Each experiment involving inhibition with targeted drugs was performed in three, and measurements without inhibitors were performed in five biological replicates. This resulted in 780 samples. Incubation with therapeutics only and dilution series of control lysated were included as controls.

2012-10-22 | E-GEOD-36324 | biostudies-arrayexpress

The gene expression pattern of mice fed the resveratrol-enriched rice DJ526 was very different from mice fed either resveratrol or Dongjin rice alone

Project description:The gene expression profiling analyses by DNA chip showed that the gene expression pattern of mice fed resveratrol-enriched rice DJ526 was very different from mice fed either resveratrol or Dongjin rice alone, respectively, modifying expression of genes related to aging regulation, cell differentiation, extracellular matrix, neurogenesis, or secretion. (1) Ctrl (The control mice fed a NFD in which the carbohydrate source was corn starch and sucrose), (2) RS (resveratrol mice fed a NFD in which the carbohydrate source was corn starch and sucrose except containing resveratrol), (3) DJ (Dongjin mice fed a NFD in which the corn starch and sucrose were replaced with Dongjin rice), and (4) DJ526 (DJ526 mice fed a NFD in which the corn starch and sucrose were replaced with the resveratrol-enriched rice DJ526)

2016-03-12 | E-GEOD-79109 | biostudies-arrayexpress

Targeted inhibition of human breast cancer cell lines selected as model systems of ERBB2-positive/EGFR high breast cancer [RPPA-SKBR3]

2012-10-22 | E-GEOD-36326 | biostudies-arrayexpress