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Whole genome bisulfite sequencing of two/three-week-old Arabidopsis thaliana plants of the genotypes Col-0, nrpe1-11 and ros1-4.

ABSTRACT: Whole genome bisulfite sequencing of two/three-week-old Arabidopsis thaliana plants of the genotypes Col-0, nrpe1-11 and ros1-4.

PROVIDER: PRJNA820865 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18508333_1.fastq.gz	Fastqsanger.gz
	SRR18508333_2.fastq.gz	Fastqsanger.gz
	SRR18508334_1.fastq.gz	Fastqsanger.gz
	SRR18508334_2.fastq.gz	Fastqsanger.gz
	SRR18508335_1.fastq.gz	Fastqsanger.gz

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Whole genome bisulfite sequencing of two/three-week-old Arabidopsis thaliana plants of the genotypes Col-0, nrpe1-11 and ros1-4.

Project description:This study used the mutants nrpe1-11 and ros1-4 to assess the impact of RNA-directed DNA methylation (RdDM) and ROS1 on the Arabidopsis thaliana (ecotype Col-0) methylome.

2022-11-07 | GSE199625 | GEO

MethlyC-Seq of Col-0 (wild type, WT), nrpd1-3, nrpe1-11, ros1-4 single mutants and ros1-4nrpd1-3 double mutant

Project description:Using MethylC-Seq to provide single-base resolution of DNA methylation status in WT, nrpd1-3, nrpe1-11, ros1-4 single mutants and ros1-4nrpd1-3 double mutant

2016-11-01 | GSE72280 | GEO

Nanopore sequencing of estradiol and DMSO treated XVE:ROS1-YFP plants

Project description:Transgenic plants carrying an estradiol-inducible ROS1-YFP construct (XVE:ROS1-YFP) were subjected to long-read sequencing (Oxford Nanopore Technologies) to assess the global impacts of ROS1 activity on the methylome of Arabidopsis thaliana (ecotype Col-0).

2022-11-07 | GSE211295 | GEO

Expression analysis of Arabidopsis thaliana wild-type Col-0 and selected RNA silencing mutant plants

Project description:Investigation of whole genome gene expression level changes in several Arabidopsis thaliana mutants (nrpd1, nrpe1, ros1 dml2 dml3) compared to wild-type Col-0. The mutants analyzed in this study are further described in Le et al. 'DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis' . Genome Biology (in press). A twelve chip study using total RNA recovered from three week-old plants grown on Murashige Skoog sucrose agar. The number of biological replicates for each plant genotype were as follows: Col-0 (3 biological replicates), rdd (2), nrpd1 (2) and nrpe1 (2) respectively. Each array contains 60-mer probes targeting 39,042 genes (TAIR 9.0) with 4 probes per gene.

2014-08-20 | E-GEOD-60508 | biostudies-arrayexpress

Whole genome bisulfite sequencing of rdm16ros1, ros1, nrpd1ros1 mutants and C24 wild-type

Project description:Using whole genome bisulfite sequencing to provide single-base resulution of DNA methylation status in rdm16ros1, ros1, nrpd1ros1 mutants and examine the effect of RDM16 on DNA methylation 4 samples examined: C24 wild type with RD29A-LUC transgene, rdm16ros1 double mutant, ros1 mutant, nrpd1ros1 mutant (all in C24 background with RD29A-LUC transgene)

2013-09-27 | E-GEOD-44417 | biostudies-arrayexpress

mRNA-seq of ros1-3 and ros1-4 with ABA treatment

Project description:To survey transcriptome changes by the mutations of a DNA demethylase ROS1 responding to a phytohormone abscisic acid, we performed the Next-gen sequencing (NGS) associated RNA-seq analysis. Two ROS1 knockout lines (ros1-3, ros1-4; Penterman et al. 2007 [PMID: 17409185]) with the wild-type Col line (wt) were subjected. Three samples (ros1-3, ros1-4 and wt), biological triplicates, ABA or mock treatment, using Illumina HiSeq 2500 system

2016-01-15 | E-GEOD-65016 | biostudies-arrayexpress

BS-seq of ros1-3, ros1-4 with wildtype col-0

Project description:To servey the methylome changes by mutation of a DNA demethylase ROS1, we performed the Next-gen sequencing (NGS) associated whole genome bisulfite sequencing (BS-seq) analysis. Two ROS1 knockout lines (ros1-3 and ros1-4; Penterman et al. 2007 [PMID: 17409185]) were subjected in this study.

2018-12-31 | GSE64569 | GEO

mRNA-seq of ros1-3 and ros1-4 with ABA treatment

2016-01-15 | GSE65016 | GEO

Expression analysis of Arabidopsis thaliana wild-type Col-0 and selected RNA silencing mutant plants

2014-08-20 | GSE60508 | GEO

RNA Sequencing Analysis of Nicol-Het, Nicol-KO and Ros1-KO Caput Epididymal Transcriptomes.

Project description:Purpose: The goal of this study is to detect differentially expressed genes, between Nicol +/- (Nicol-Het), Nicol-/- (Nicol-KO), and Ros1-/- (Ros1-KO) caput epididymis by RNA sequencing Methods: Caput epidiymal mRNA profiles of 14-week-old Nicol-Het, Nicol-KO, and Ros1-KO mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000. Results: RNA-seq data identified differentially expressed transcripts. Conclusions: Our results show that the expression of many genes were downregulated in Nicol-KO caput epididymis compared with Nicol-Het one. The gene downregulation of Nicol-KO caput epididymis was similar to that of Ros1-KO one.

2023-02-27 | GSE206174 | GEO

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