|
| Status |
Public on Feb 09, 2017 |
| Title |
YJ suvh1 Bsseq rep2 |
| Sample type |
SRA |
| |
|
| Source name |
bisulfite converted DNA from ten-day-old YJ suvh1 seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
line: YJ suvh1
tissue: seedling
age: 10 days
|
| Growth protocol |
Plants were grown with 16hr of light
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the DNeasy Plant Mini Kit.
To generate the whole-genome bisulfite sequencing (BS-seq) libraries, genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen). One microgram of genomic DNA was sonicated into fragments 100 to 300 bp in length using a Diagenode Bioruptor. The sonicated DNA fragments were purified using the PureLink PCR Purification Kit (Invitrogen). End repair was performed using the End-It™ DNA End-Repair Kit (Epicenter) followed by purification of the Agencourt AMPure XP-PCR Purification system. 3’-end adenylation was performed at 37°C for 30 min using dATP and Klenow Fragment (3’"5’ exo-) (New England Biolabs), followed by purification using the Agencourt AMPure XP-PCR Purification system. The purified DNA was ligated with methylated adapters from the TruSeq DNA Sample Preparation Kit (Illumina). The ligation products were purified with AMPure XP beads twice. Less than 400 ng ligated product was used for bisulfite conversion using the MethylCode Kit (Invitrogen) according to the manufacturer’s guidelines, except for the addition of 12 μg carrier RNA (Qiagen) to the conversion product before column purification. The final conversion product was amplified using Pfu Cx Turbo (Agilent) under the following PCR conditions: 2 min at 95°C; 9 cycles of 15 s at 98°C, 30 s at 60°C and 4 min at 72°C; and 10 min at 72°C. The PCR product was purified using AMPure XP beads prior to a 101-cycle sequencing run (single end) on an Illumina HiSeq 2000.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The raw reads that passed the Illumina quality control steps were retained, and duplicated reads were removed prior to mapping. For BSseq, the reads were mapped to the TAIR10 genome using BS Seeker, and in-house R and Perl scripts were employed to convert the BS Seeker-aligned reads to the methylation level of every cytosine.
For BSseq, the Wiggle files contain the methylation level for each nucleotide that are calculated as the methylated number of cytosine divided by total number of cytosine.
Genome_build: TAIR10
|
| |
|
| Submission date |
Dec 31, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
shaofang Li |
| Organization name |
Beijing Academy of Agriculture and Forestry Science
|
| Department |
Beijing Vegetable Research Center
|
| Street address |
No 50, ZhanghuaLu, HAIDIAN
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100097 |
| Country |
China |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE64600 |
SUVH1, a histone methyltransferase, is required for the expression of genes targeted by DNA methylation |
|
| Relations |
| BioSample |
SAMN03274246 |
| SRA |
SRX825974 |
