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Sample GSM2101963 Query DataSets for GSM2101963
Status Public on Jul 22, 2016
Title ddm1 dcl3
Sample type SRA
Source name stage 1-9 inflorescence tissue
Organism Arabidopsis thaliana
Characteristics genotype/variation: ddm1 dcl3
Growth protocol All mutants used in this study are in the Col-0 ecotype background of Arabidopsis thaliana. Plants were grown in long-day (18 hour light) conditions at 23℃ and stage 1-12 inflorescence 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 Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina NextSeq 500
Description library strategy: MethylC-seq
Data processing Data were mapped to the TAIR10 reference genome
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: tab delimited text file, see metafile for column headers
Submission date Mar 30, 2016
Last update date May 15, 2019
Contact name Robert J Schmitz
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)
GSE79746 Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation
BioSample SAMN04594648
SRA SRX1671724

Supplementary file Size Download File type/resource
GSM2101963_Schmitzlab_allc_Arabidopsis_ddm1_dcl3.tsv.gz 165.3 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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