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Sample GSM2526529 Query DataSets for GSM2526529
Status Public on Jul 16, 2017
Title nrpd1-3 rep2
Sample type SRA
Source name 2.5 week above ground tissues
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
mutant background: nrpd1-3
transgene: N/A
Treatment protocol Transgenic lines were selected for by spraying with Basta herbicide
Growth protocol Plants were grown in soil in long day conditions (16h light, 8 hours dark)
Extracted molecule genomic DNA
Extraction protocol CTAB extraction of genomic DNA from 2.5 week above ground tissues
Illumina TruSeq DNA methylation Kit (product number: EGMK81312)
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina NextSeq 500
Description Index 6
Data processing Base-calling, adapter trimming, and size selection (>35bp) was completed with bcl2fastq v2.16.0.10
Methylation end bias was removed and reads were quality filtered using cutadapt v. 1.9.1 with the commands: cutadapt -U 7 -u 2 -q 25
Filtered reads were mapped to the TAIR10 genome and mapped reads were deduplicated using Bismark 0.16.1 using default settings.
Methylation status of each cytosine was extracted from mapped reads using Bismark_methylation_extractor with the commands: bismark_methylation_extractor -p --bedGraph --CX -cutoff 5 --cytosine_report --CX
Methylation status of each cytosine in the CHH context was extracted from the bismark_methylation_extractor output and used as input to the R package, methylkit v. 0.9.5 to define differentially methylated regions (DMRs) relative to Col-0. The genome was split into 300 base pair sliding windows with a step size of 200 base pairs and a minimum coverage requirement for each window of 10 informative cytosines with at least 5 read coverage each. Only regions that had coverage in each sample were utilized for calculation of DMRs. Significant hypo-DMRs were defined as those regions with a minimum 10% or 25% decrease in methylation relative to Col-0 and a q-value of less than or equal to 0.01.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited text files that include methylation status of cytosines in the CHH context with at least 5 read coverage. Format for input to R package methylkit
Submission date Mar 08, 2017
Last update date May 15, 2019
Contact name Jered Wendte
Organization name Indiana University
Street address 915 E. 3rd Street
City Bloomington
State/province IN
ZIP/Postal code 47405
Country USA
Platform ID GPL19580
Series (2)
GSE95823 Assessment of the Pol IV largest subunit, NRPD1, DeCL domain deletion construct to rescue Pol IV-dependent DNA methylation in the nrpd1-3 mutant (Bisulfite-Seq).
GSE95825 Functional analysis of the Pol IV DeCL domain
BioSample SAMN06547434
SRA SRX2620193

Supplementary file Size Download File type/resource
GSM2526529_d1.3_I6_CHH.txt.gz 103.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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