|
| Status |
Public on May 22, 2020 |
| Title |
W82_Nodule_22dpi_Rep2_MethylC-seq |
| Sample type |
SRA |
| |
|
| Source name |
Bradyrhizobium diazoefficiens USDA110
|
| Organism |
Glycine max |
| Characteristics |
cultivar: Williams 82
tissue: Nodule
age: 25 days
|
| Treatment protocol |
B. diazoefficiens USDA110 cultures (4.5 x 106 cells/ml) were poured over each tray. After inoculation, the trays were kept in a growth chamber that was maintained at a constant temperature of 28° C with a light intensity of 500 mmol of photons per square meter per second, and a 12-h light period.
|
| Growth protocol |
The seeds were surface-sterilized in 50% bleach (2.5% NaClO). Approximately 200 seeds were planted in large plastic tray (50 x 28 x 15 cm deep) filled with vermiculite and the seeds were allowed to germinate in dark for 3 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using DNAeasy Plant Mini Kit (Qiagen) following the manufacturer’s instructions.
Whole genome methylC-seq libraries were constructed following the protocol from Illumina TruSeq Library Prep kit (Illumina, San Diego, CA)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: MethylC-Seq
Adapters and low quality reads below phred threshold of 33 were removed using Trimmomatic.
Reads were aligned to the soybean reference genome (Wm82.a2.v1) using Bismark.
Differentially methylated cytosines were identified using R bioconductor package methylKit.
Differentially methylated regions were mapped to various genic regions using R Bioconductor package rtracklayer.
Genome_build: Wm82.a2.v1
|
| |
|
| Submission date |
Aug 19, 2019 |
| Last update date |
May 22, 2020 |
| Contact name |
Sarbottam Piya |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Tennessee
|
| Department |
Plant Science
|
| Lab |
Hewezi Lab
|
| Street address |
2431 Joe Johnson Dr.
|
| City |
Knoxville |
| State/province |
Tennessee |
| ZIP/Postal code |
37996 |
| Country |
USA |
| |
|
| Platform ID |
GPL19246 |
| Series (2) |
| GSE135969 |
Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity |
| GSE135972 |
Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity |
|
| Relations |
| BioSample |
SAMN12600384 |
| SRA |
SRX6734533 |
