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Sample GSM2590475 Query DataSets for GSM2590475
Status Public on Apr 28, 2017
Title nrpd1_wgbs
Sample type SRA
 
Source name 2-week-old seedlings
Organism Arabidopsis thaliana
Characteristics genotype: nrpd1-3
Growth protocol On 1/2 MS plates at 22ÂșC with 12h:12h day-night cycle in the growth chamber
Extracted molecule genomic DNA
Extraction protocol Genomic DNA extracted from 2-week-old seedlings using the Qiagen Plant DNeasy Maxi kit
Constructed using Illumina TruSeq DNA Library Prep Kit
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
 
Data processing Basecalling performed using CASAVA v1.8
Adapter sequences and low quality bases (q<30) removed using trim_galore v0.4.0 and catadapt v1.8.3
Reads aligned to the Arabidopsis TAIR10 genome using bsmap 2.74
Genome_build: TAIR10
Supplementary_files_format_and_content: tdf files of cytosine methylation ratio at single basepair resolution, only cytosines with a coverage > 4 are included
 
Submission date Apr 27, 2017
Last update date May 15, 2019
Contact name Heng Zhang
E-mail(s) zhangheng@sibs.ac.cn
Organization name Chinese Academy of Sciences
Department Shanghai Center for Plant Stress Biology
Street address 3888 Chenhua Rd, Gate 3
City Shanghai
ZIP/Postal code 201602
Country China
 
Platform ID GPL13222
Series (2)
GSE98283 The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci (Bisulfite-Seq)
GSE98286 The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci
Relations
BioSample SAMN06842155
SRA SRX2766968

Supplementary file Size Download File type/resource
GSM2590475_nrpd1_wgbs.tdf 141.6 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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