|
| Status |
Public on May 22, 2020 |
| Title |
W82_Nodule_12dpi_Rep3_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Bradyrhizobium diazoefficiens USDA110
|
| Organism |
Glycine max |
| Characteristics |
cultivar: Williams 82
tissue: Nodule
age: 15 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 |
total RNA |
| Extraction protocol |
mRNA was isolated using magnetic mRNA isolation kit (NEB).
RNA-seq libraries were prepared using NEBnext mRNA library prep master mix (NEB) following manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Quality of paired-ended reads was accessed using FastQC (version 0.11.4).
Adapter sequences and low-quality reads were removed using Trimmomatic (version 0.35).
TOPHAT v.2.0.13 was used to map the reads to the soybean reference genome (Wm82.a2.v1).
Reads mapped to multiple loci were discarded and numbers of uniquely mapped reads per gene were determined using HTSeq.
Differentially expressed genes were identified the R package DESEQ2.
Python-based package QoRTs was used for counting sequencing reads spanning exons for every gene.
Differentially spliced transcripts were identified using R package JunctionSeq.
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) |
| GSE135971 |
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 |
SAMN12600406 |
| SRA |
SRX6734549 |
