|
| Status |
Public on Oct 30, 2012 |
| Title |
BS-seq of roots |
| Sample type |
SRA |
| |
|
| Source name |
roots
|
| Organism |
Glycine max |
| Characteristics |
developmental stage: 14 days after germination
tissue: roots
|
| Growth protocol |
Soybean seeds of Glycine max cultivar Heinong44 were respectively planted in the experimental station and growth chambers in Beijing on May. Soybean cotyledons were dissected from seeds of 20 days after flowering (DAF). Roots, stems, and leaves were harvested from the plants cultivated for 14 days in growth chambers.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, 5 ug genome DNA was extracted from the tissue of roots, stems, leaves, and cotyledons using DNeasy Plant Mini Kit (Qiagen), followed by fragmentation to 50-500 bp with a Bioruptor (Diagenode Sparta). End repair and adding an ‘A’ base to the 3’ end were performed to the DNA fragment and then methylated DNA adapter was ligated to the product. The adapter-ligated DNA of 150-200 bp was purified from agarose gel, followed by two treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen).The bisulfite-converted DNA was amplified by 18 cycles of PCR using uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Stratagene) and purified with PCR purification kit (Qiagen).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
root_site.txt; genome build: Glyma1.0
We first obtained the two converted genome sequences, which were respectively derived by conversion of C (cytosine) to T (thymidine) and G (guanine) to A (adenosine). Reads with the conversion of C to T were mapped to the two converted genome sequences by Burrows-Wheeler Aligner (BWA) with no more than two nucleotides mismatch. We extracted the first 75 bases of unmapped reads and performed the alignment again. Only reads mapped to unique site were reserved for further analysis. The Perl scripts were used to recover the converted reads to original sequence and calculated the numbers of C and T for each C in the genome sequence. Methylated cytosine was defined as below: cytosine was covered by no less than two reads, and the sequencing number of C was more than 80% of sequencing number of C plus T.
Column 1: chromosome;Column 2: cytosine location; Column 3: forward strand or reverse strand. +: forward strand, -: reverse strand; Column 4: cytosine type: CG, CHG or CHH; Column 5: sequencing read number of methylated cytosines ;Column 6: sequencing read number of unmethylated cytomsines.
|
| |
|
| Submission date |
Jan 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jinsong Zhang |
| E-mail(s) |
jszhang@genetics.ac.cn
|
| Organization name |
IGDB
|
| Street address |
No.1 West Beichen Road,Chaoyang District
|
| City |
beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL15087 |
| Series (2) |
| GSE34849 |
Analysis of soybean DNA methylomes shows CHH hypermethylation enhances gene expression in cotyledons of developing seeds [methylome] |
| GSE34875 |
Analysis of soybean DNA methylomes shows CHH hypermethylation enhances gene expression in cotyledons of developing seeds |
|
| Relations |
| SRA |
SRX113929 |
| BioSample |
SAMN00769635 |
