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| Status |
Public on Jul 07, 2014 |
| Title |
Col A BSseq |
| Sample type |
SRA |
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| Source name |
Col A BSseq
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
tissue: ten-day-old seedlings
genotype: wild type
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| Growth protocol |
Arabidopsis thaliana seeds were surface sterilized by either 30% bleach or fumigated in an airtight container with a solution containing 50 mL of 100% bleach and 8% HCl for six hours. After, the seeds were planted on half-strength MS-agar plates containing 1% sucrose (no sucrose was added in plates used for chemical screening to minimize fungal growth), stratified at 4°C for two days and moved into a growth chamber. Plants were grown under continuous light at 23°C. All experiments were performed with ten-day-old seedlings.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
BSseq: approximately 1μg of genomic DNA was sonicated to 100~300 bp with Diagenode Bioruptor using the following settings: intensity=high, on=30s, off=30s, total time=60min. Sonicated DNA was purified using the PureLink® PCR Purification Kit (Life Sciences). Purified DNA was end-repaired using the End-It kit (Epicentre) except that dCTP was not included in the reaction. The end-repaired DNA was purified with Agencourt AMPure XP beads (Beckman Coulter), A-tailed with dATP and Klenow 3’-5’ exo- (New England Biolabs) for 30 min at 37°C and then purified with Agencourt AMPure XP beads.
BSseq: The purified DNA was ligated overnight at 16°C to genomic DNA adapters from the Illumina Truseq DNA sample preparation kit with T4 DNA Ligase (New England Biolabs). Ligation products were purified with AMPure XP beads (Beckman) twice. Less than 400ng ligated product was converted using the MethylCode Kit (Invitrogen) following the manufacturer’s guidelines except that 12ug carrier RNA (Qiagen) was added into the conversion product before column purification. The final conversion product was amplified using PfuTurbo Cx Hotstart DNA Polymerase (Agilent) under the following PCR conditions (2 minutes at 95°C, 9 cycles of 15 seconds at 98°C, 30 seconds at 60°C, 4 minutes at 72°C and 10 minutes at 72°C). The PCR product was purified with AMpure XP beads to obtain the final library DNA. BS-seq libraries were sequenced at 101 cycles using an Illumina HiSeq 2000.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava software used for basecalling.
Raw data from Illumina sequencing were filtered to remove reads that failed to pass the Illumina quality control and to condense multi-copy reads to a single copy. Hereafter, the reads were mapped to TAIR 10 Arabidopsis genome as well as a C-to-T converted genome using BS_Seeker with default settings. Only perfectly and uniquely mapped reads were retained. The BS_Seeker results were converted to txt files by a perl script built in house.
Genome_build: TAIR10, and pseudo-Ler genome generated by incorporating the Ler polymorphisms into the Tair10 Columbia genome (ftp://ftp.arabidopsis.org/Polymorphisms/Ecker_ler.homozygous_snp.txt)
Supplementary_files_format_and_content: txt file, which has six columns: chr,postion,C context, strand, methylated C number, Total C number
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| Submission date |
Sep 09, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Lei Gao |
| E-mail(s) |
[email protected]
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| Organization name |
shenzhen university
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| Department |
College of Life Sciences
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| Street address |
Nanhai Ave 3688
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| City |
shenzhen |
| State/province |
guangdong |
| ZIP/Postal code |
518060 |
| Country |
China |
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| Platform ID |
GPL13222 |
| Series (2) |
| GSE50691 |
DNA Topoisomerase 1α Promotes RNA-directed DNA Methylation and Histone Lysine 9 Dimethylation at Transposable Elements in Arabidopsis [Bisulfite-Seq] |
| GSE50720 |
DNA Topoisomerase 1α Promotes RNA-directed DNA Methylation and Histone Lysine 9 Dimethylation at Transposable Elements in Arabidopsis |
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| Relations |
| BioSample |
SAMN02351222 |
| SRA |
SRX347182 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1226506_Col_A.methy.txt.gz |
156.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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