|
| Status |
Public on Oct 07, 2020 |
| Title |
Control Dawn 3h Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Rice Leaf Tissue
|
| Organism |
Oryza sativa Indica Group |
| Characteristics |
group: Control
tissue: Leaf Tissue
time point: Dawn 3h
|
| 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 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 leaf tissue samples were first grinded. 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 |
2-3h_C.1
|
| 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 normilized to counts per million.
Genome_build: MH63RS1
Supplementary_files_format_and_content: http://rice.hzau.edu.cn/cgi-bin/gb2/gbrowse_details/
Supplementary_files_format_and_content: Raw Counts
|
| |
|
| Submission date |
Oct 06, 2020 |
| Last update date |
Oct 09, 2020 |
| Contact name |
Montana Knight |
| E-mail(s) |
mknight@ncsu.edu
|
| Organization name |
North Carolina State University
|
| Department |
Genomic Sciences Graduate Program
|
| Lab |
Nielsen/Doherty
|
| Street address |
Campus Box 7566
|
| City |
RALEIGH |
| State/province |
NC |
| ZIP/Postal code |
27695 |
| Country |
USA |
| |
|
| Platform ID |
GPL21027 |
| Series (1) |
| GSE159073 |
Temporal analysis of mRNA from leaf tissue in field grown rice |
|
| Relations |
| BioSample |
SAMN16379120 |
| SRA |
SRX9248499 |
