|
| Status |
Public on Oct 24, 2017 |
| Title |
Wild type 18 DAP embryo BS-seq,rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryo
|
| Organism |
Zea mays |
| Characteristics |
cultivar: W22 inbred line
developmental stage: 18 days after pollination (DAP)
tissue: embryo
genotype: WT
|
| Treatment protocol |
Embryos were isolated and collected from 18 DAP developing kernel by manual dissection.
|
| Growth protocol |
Plants were grown in field from 2014-2016
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using CTAB method.
10 ug of genomic DNA was sheared to fragments between 300 and 500 bp. The fragments were subject to end repair, dA tailing, and ligating to methylated adapters, followed by bisulfate conversion.The bisulfate converted library were then PCR amplified (13 cycle) and purified, and sequenced on Illumina Hiseq 2500 platform.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
BS-seq_WT.CGmap.bed
|
| Data processing |
Base calling was performed following the standard Illumina protocol.
Bisulfite sequencing reads were trimmed to remove adaptor sequence and low-quality sequence using Trim_galore,then aligned to the B73 reference genome version 2 using BS-seeke2 with default parameter.Then information of the methylation level of each cytosine was extracted using specific software contained by BS-seeker2
genome build: B73 reference genome version 2
processed data files format and content: CGmap file was generated by BS-seeker2. Columns are: 1. chromosome, 2. nucleotide on Watson (+) strand, 3. position, 4. context (CG/CHG/CHH), 5. dinucleotide context (CA/CC/CG/CT), 6. methylation-level = #_of_C/ (#_of_C + #_of_T), 7. #_of_C (methylated C, the count of reads showing C here), 8. #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here).
|
| |
|
| Submission date |
Oct 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jincheng Long |
| E-mail(s) |
longjincheng1990@163.com
|
| Phone |
+8613001298733
|
| Organization name |
China Agricultural University
|
| Department |
National Maize improvement center
|
| Lab |
Yan He'Lab
|
| Street address |
Hai Dian district ,Yuanmingyuan Road.Beijing
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
10083 |
| Country |
China |
| |
|
| Platform ID |
GPL17628 |
| Series (1) |
| GSE105780 |
Decrease in DNA methylation 1(DDM1) is required for the establishement of CHH islands in maize |
|
| Relations |
| BioSample |
SAMN07822311 |
| SRA |
SRX3312757 |
