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Sample GSM1571850 Query DataSets for GSM1571850
Status Public on May 13, 2015
Title MA2_3_G17_82_r1
Sample type SRA
 
Source name leaf tissue
Organism Arabidopsis thaliana
Characteristics cultivar: Col-0
tissue: leaf
age: ~3 week old plants
Growth protocol Arabidopsis thaliana were grown in long days (16 hours of light) at 24C
Extracted molecule genomic DNA
Extraction protocol Genomic DNA (gDNA) was purified from Arabidopsis thalina leaf tissue using a Qiagen DNease Plant Kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions. MethylC-Seq libraries were constructed according to Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. (2014) MethylC-seq: Base resolution whole genome bisulfite sequencing library preparation. Nature Protocols (in press)
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina NextSeq 500
 
Data processing Data were mapped to the Arabidopsis thaliana reference genome version 10 (TAIR10)
MethylC-seq analysis were performed as described in Schmtiz et al. Epigenome-wide inheritance of DNA methylation variants in a recombinant inbred population. Genome Research (2013).
Genome_build: TAIR10
Supplementary_files_format_and_content: MA[pedigreeID]_[experimentID]_G[generationsFromCommonFounder]_[lineNumberID]_r[replicate].txt.gz contains for every cytosine in the TAIR 10 genome: Chromosome, strand, position in the genome, context, methylated coverage and total coverage Uncompressed data is in a tab delimited format. Format, per column: <chr TAIR10> <strand TAIR10> <C position TAIR10> <sequence context of the cytosine> X=CG, Y=CHG and Z=CHH <methylated coverage> <total coverage>
 
Submission date Dec 23, 2014
Last update date May 15, 2019
Contact name Robert J Schmitz
E-mail(s) schmitz@uga.edu
Organization name University of Georgia
Department Genetics
Street address B416 Davison Life Sciences
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
 
Platform ID GPL19580
Series (1)
GSE64463 Rate, spectrum, and evolutionary dynamics of spontaneous epimutations
Relations
BioSample SAMN03272750
SRA SRX835907

Supplementary file Size Download File type/resource
GSM1571850_MA2_3_G17_82_r1.txt.gz 155.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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