|
| Status |
Public on Aug 15, 2019 |
| Title |
WNT Dawn 3.5h Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Rice Panicle
|
| Organism |
Oryza sativa Indica Group |
| Characteristics |
variety: IR64
developmental stage: 50% flowering
tissue: Panicle
treatment: WNT
time point: Dawn 3.5h
|
| Treatment protocol |
Plants were grown in a field setting. WNT were treated with IR heater at night. 24C, 26C, 28C, and 30C rice were treated with field tents for increased night temperatures.
|
| Growth protocol |
An IR64 land variety was grown on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue samples were stored at -80C until needed. The panicle samples were first grinded in liquid nitrogen with a metal pestle. The tissue then lyophilized at -60C overnight before RNA extractions. Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen) with the recommended RLT lysis buffer. The RNA extraction provided protocol was followed the inclusion of DNase step. RNA concentration was then measured with NANOdrop 2000. 2ug of RNA was used with NEBNext Poly(A) Magnetic mRNA isolation kit (NEB). Oligo(dT) attached to magnetic beads isolate mRNA by attaching to ploy(A) modified mRNA.
RNA libraries were prepared for sequencing using NEB ultra directional library prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
2-3.5h_WNT.1
processed data file: Pannicle_timecourse_WNT.csv
|
| Data processing |
Trimmed files were aligned using Hisat v2. MH63 (rigw.com). The resulting bam files were then piped to htseq count version 0.6.0. Using the options -f bam, -s reverse, and -m union counts per gene were generated for the annotated genes in MH63. Counts were than normalized to counts per million.
Genome_build: MH63RS1
Supplementary_files_format_and_content: Pannicle_timecourse_WNT.csv: Comma-separated text file includes raw counts.
Supplementary_files_format_and_content: Pannicle_gradient_24_26_28_30C.csv: Comma-separated text file includes raw counts.
|
| |
|
| Submission date |
Aug 14, 2019 |
| Last update date |
Aug 15, 2019 |
| Contact name |
Jigar Desai |
| E-mail(s) |
jdesai@ncsu.edu
|
| Phone |
7042147914
|
| Organization name |
NCSU
|
| Department |
Biochemistry
|
| Lab |
Doherty Lab
|
| Street address |
128 Polk Hall
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27695 |
| Country |
USA |
| |
|
| Platform ID |
GPL21027 |
| Series (1) |
| GSE135847 |
Temporal analysis of mRNA from panicle tissue from field grown rice under high nighttime temperatures |
|
| Relations |
| BioSample |
SAMN12574379 |
| SRA |
SRX6716863 |
