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Sample GSM2101039 Query DataSets for GSM2101039
Status Public on Jun 20, 2018
Title WGBS_trisomy3_77
Sample type SRA
Source name #77 trisomy3
Organism Arabidopsis thaliana
Characteristics tissue: leaves
ploidy: trisomy3
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from rosette leaves using a Wizard Genomic DNA Purification kit A1120 (Promega, USA). The procedure involves lysis of isolated nuclei, RNase digestion, protein precipitation, centrifugation, precipitation of DNA from the supernatant using isopropanol, followed by a wash step with 70% ethanol. After pelleting the precipitated DNA by centrifugation, it was dried under a vacuum and rehydrated in sterile nuclease free water.
genomic DNA was sheared by sonication to generate DNA fragments in the 100-300 bp size range. Bisulfite treatment and library preparation were carried out as described (Feng et al. 2011), except that the EpiTect Fast kit (QIAGEN) was utilized for bisulfite treatment. The resulting libraries were sequenced with Illumina sequencing technology (Illumna NextSeq500 sequencer).
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina NextSeq 500
Data processing BS-seq reads were aligned to the TAIR10 genome using BS Seeker2
If multiple alignments mapped to the same location only one is kept.
genome build: TAIR10
processed data files format and content: Processed data (CGmap) is in text format. column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.
Submission date Mar 29, 2016
Last update date May 15, 2019
Contact name Pao-Yang Chen
Organization name Academia Sinica
Department Institute of Plant and Microbial Biology
Lab Pao-Yang Chen
Street address 128 Sec. 2, Academia Rd, Nankang,
City Taipei
ZIP/Postal code 115
Country Taiwan
Platform ID GPL19580
Series (1)
GSE79676 Bisulfite-Seq and RNA-seq profiling of Arabidopsis aneuploids
BioSample SAMN04589721
SRA SRX1668398

Supplementary file Size Download File type/resource
GSM2101039_FMC0066_R1_unique.fastq.ara.CGmap.txt.gz 139.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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