|
| Status |
Public on Jun 01, 2017 |
| Title |
iF_BS-seq |
| Sample type |
SRA |
| |
|
| Source name |
Callus
|
| Organism |
Oryza sativa Indica Group |
| Characteristics |
rice cultivar: Indica Rice 64
tissue culture stage: Failed Regeneration
time point: TF
|
| Treatment protocol |
The callus samples were collected at different time points of culture starting with embryonic stage (T0). N6D medium was used for callus induction of both cultivars; induced calli were transferred to fresh N6D medium for subsequent callus growth. Finally calli were transferred to REIII M2 medium (MS salt with vitamin, 1g/L casein hydrolysate, 3% sucrose, 3% sorbitol, 0.02 mg/L NAA, 2mg/L BAP, pH5.8 0.4% gelrite) for regeneration.
|
| Growth protocol |
Seeds of TNG67 and IR64 were surface-sterilized in 70% ethanol for 1 min and rinsed with distilled water. The sterilized seeds were soaked in 2.5% sodium hypochlorite (NaClO; The Clorox Co., Oakland, CA, USA) containing 0.2% Tween 20 (Sigma-Aldrich, St. Louis, MO, USA) for 15 min in a rotator followed by washing with sterile ddH2O. After surface sterilization, seeds were sown on N6D media (N6 salt, Vitamin B5, 3% sucrose, 2.5 mg/L 2,4-D pH 5.8 0.4% gelsite) for callus induction.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Rice calli were ground using pestle and mortar in the presence of liquid nitrogen for extraction of genomic DNA (gDNA) followed by purification using DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany).
To obtain fragments ranging between 50 and 350 bp the gDNA was sonicated. The fragmented DNA was then used for library preparation using Illumina's library preparation kits. Premethylated adapter ligated fragments were bisulfite converted using the EZ DNA methylation kit (Zymo Research). Resulted libraries were then subjected to PCR amplification prior to sequencing on the Illumina HiSeq 2000 sequencers at National Center for Genome Medicine at Academia Sinica. The genome size of rice is about 466 MB and sequencing was done in enough lanes to reach >20x per sample
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
BS-seq
|
| Data processing |
BS-Seq reads were aligned to the MSU7 genome using BS Seeker2
genome build: MSU7
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.
|
| |
|
| Submission date |
Jun 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Moloya Gohain |
| E-mail(s) |
moloyandri@gmail.com
|
| Organization name |
ACADEMIA SINICA
|
| Department |
INSTITUTE OF PLANT AND MICROBIAL BIOLOGY
|
| Lab |
DR. PAO-YANG CHEN LABORATORY
|
| Street address |
128, SEC.2 ACADEMIA ROAD, NANGANG DISTRICT
|
| City |
Taipei |
| State/province |
Taipei |
| ZIP/Postal code |
11529 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL14553 |
| Series (1) |
| GSE82138 |
Dynamics of the transcriptome and methylome during the regeneration of rice |
|
| Relations |
| BioSample |
SAMN05195278 |
| SRA |
SRX1815124 |
