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| Status |
Public on Jun 20, 2018 |
| Title |
WGBS_triploid_165 |
| Sample type |
SRA |
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| Source name |
#165 triploid
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaves
ploidy: triploid
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| 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).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
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| 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.
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| Submission date |
Mar 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Pao-Yang Chen |
| Organization name |
Academia Sinica
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| Department |
Institute of Plant and Microbial Biology
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| Lab |
Pao-Yang Chen
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| Street address |
128 Sec. 2, Academia Rd, Nankang,
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| City |
Taipei |
| ZIP/Postal code |
115 |
| Country |
Taiwan |
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| Platform ID |
GPL19580 |
| Series (1) |
| GSE79676 |
Bisulfite-Seq and RNA-seq profiling of Arabidopsis aneuploids |
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| Relations |
| BioSample |
SAMN04589747 |
| SRA |
SRX1668403 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2101044_FMC0071_R1_unique.fastq.ara.CGmap.txt.gz |
140.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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