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Sample GSM2472677 Query DataSets for GSM2472677
Status Public on Jul 24, 2017
Title Line 49x69 - F2-16
Sample type SRA
 
Source name leaf tissue
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
tissue: leaf
age: ~3 weeks old
Growth protocol All samples in this study are the Col-0 ecotype of Arabidopsis thaliana. Plants were grown in long-day (16 hour light) conditions at 24℃ and 3 week old leaf tissue was used for all experiments and sequencing.
Extracted molecule genomic DNA
Extraction protocol DNA was isolated using fractional precipitation followed by phenol-chloroform extraction and RNase A treatment. 1ug of DNA was used to prepare libraries as previously described (Urich et al. 2015).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description MA-cross_line49-69-F2-16
Data processing Library strategy: MethylC–seq
Data were mapped to the TAIR10 reference genome
MethylC-seq analysis were performed as described in Schultz, M. D. et al. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature 523, 212-216 (2015).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab delimited text file; <chromosome> <cytosine position> <strand> <CNN (N = A, T, C, G)> <methylated cytosines at this site> <mapped cytosines at this site> <binomial test, 1 means methylated, 0 means unmethylated>
 
Submission date Jan 30, 2017
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)
GSE94298 Stable Inheritance of Spontaneous Epialleles in Arabidopsis thaliana
Relations
BioSample SAMN06282877
SRA SRX2528569

Supplementary file Size Download File type/resource
GSM2472677_allc_line49-69-F2-16.tsv.gz 170.9 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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