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Sample GSM1199120 Query DataSets for GSM1199120
Status Public on Jul 10, 2014
Title idm2_MethylC-Seq_rep2
Sample type SRA
 
Source name Seedlings
Organism Arabidopsis thaliana
Characteristics genotype: idm2 mutant
developmental stage: 14 day-old seedlings
Extracted molecule genomic DNA
Extraction protocol idm2 samples: Libraries were prepared according to a published protocol (Lister et al., 2008). Briefly, Genomic DNA was extracted from 14-d-old seedlings. Sonicated DNA was end-repaired by using End Repair Enzyme Mix (NEB, #E6041A). The blunt end DNA were treated with Klenow fragment (NEB, #E6044A) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Unmethylated cytosine residues were converted to uracil by EpiTect bisulfite Kit (Qiagen, 59104) after adaptor ligation. After bisufite treated DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 250~350 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols in KAUST(King Abdullah University of Science and Technology)
idm1idm2 sample: Genomic DNA was extracted from 14-d-old seedlings and sent to BGI (Shenzhen, China) for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina Genome Analyzer IIx
 
Description treated with bisulfite
Data processing idm2 samples: Each raw read was first trimmed to the longest contiguous read segment with Phred quality score>=20 (using DynamicTrim from the SolexaQA software, Cox et al, 2010) and then trimmed for the adaptor sequence if exists using an inhouse perl script. We mapped paired reads and singleton reads (when read from the other end was discarded due to low quality) to the Arabidopsis genome (TAIR10) using BRAT with parameters -m 2 -i 0 -a 1000.
idm1idm2 double mutant: Basecalling, trimming for low quality reads and adaptor sequence were done by BGI (Shenzhen, China); Clean reads were mapped to TAIR10 using BRAT-BW with parameters -m 2 -i 0 -a 1000.
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 Jul 31, 2013
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 GPL11221
Series (1)
GSE49421 MethylC-Seq of idm2 single mutant and idm1idm2 double mutant
Relations
BioSample SAMN02298436
SRA SRX330289

Supplementary file Size Download File type/resource
GSM1199120_idm2_rep2_Lane6_JKZ12_NCBI_depth4_mCG.wig.gz 16.9 Mb (ftp)(http) WIG
GSM1199120_idm2_rep2_Lane6_JKZ12_NCBI_depth4_mCHG.wig.gz 17.9 Mb (ftp)(http) WIG
GSM1199120_idm2_rep2_Lane6_JKZ12_NCBI_depth4_mCHH.wig.gz 77.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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