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Sample GSM2365448 Query DataSets for GSM2365448
Status Public on Dec 29, 2016
Title hdp2-2-1
Sample type SRA
 
Source name Seedlings
Organism Arabidopsis thaliana
Characteristics genotype/variation: hdp2-2
Extracted molecule genomic DNA
Extraction protocol The genomic DNA was extracted from 1 gram of 14-day-old seedlings using the Plant DNeasy Maxi Kit from Qiagen. And 5 µg of gDNA was used for library construction using Illumina’s standard DNA methylation analyses protocol and the TruSeq DNA sample preparation kit. The samples were sequenced in the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) with Illumina HiSeq2500.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2500
 
Data processing Reads were mapped to TAIR10 using BRAT-BW v2.0.1 with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position ( unconverted_C / ( converted_C+ unconverted_C ) ).
 
Submission date Oct 28, 2016
Last update date May 15, 2019
Contact name Jian-Kang Zhu
E-mail(s) zhu132@purdue.edu
Organization name Purdue University
Department Department of Horticulture and Landscape Architecture
Street address 625 Agriculture Mall Dr.
City West Lafayette
State/province IN
ZIP/Postal code 47907
Country USA
 
Platform ID GPL17639
Series (2)
GSE89294 Whole genome bisulfite sequencing of hdp1-1 and hdp2-1and other relative mutants (Col-0 background)
GSE89320 A Pair of Transposon-derived Proteins Function in A Histone Acetyltransferase Complex for Active DNA Demethylation
Relations
BioSample SAMN05954304
SRA SRX2310511

Supplementary file Size Download File type/resource
GSM2365448_meth_CHG_hdp2-2-1.wig.gz 15.4 Mb (ftp)(http) WIG
GSM2365448_meth_CHH_hdp2-2-1.wig.gz 70.0 Mb (ftp)(http) WIG
GSM2365448_meth_CpG_hdp2-2-1.wig.gz 14.5 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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