|
| Status |
Public on Sep 01, 2017 |
| Title |
M202 - midday - rep 4 |
| Sample type |
SRA |
| |
|
| Source name |
15+ d old whole shoots
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
genotype: M202
time point: midday
|
| Treatment protocol |
Plants were submerged in 121 L bins, in which water was allowed to equilibrate to ambient temperature for 24 h before submergence. Submergence began at ZT 6:00 and continued for 72 h, at which time plants were placed back on the greenhouse bench for reoxygenation. Whole shoots were harvested and flash-frozen in liquid N2 immediately upon desubmergence (3d_sub) at midday (ZT9:00), at dusk (ZT15:30), midnight (ZT19:45), dawn (ZT0), and again at midday 24 h following desubmergence (ZT9:00).
|
| Growth protocol |
Rice seeds (Oryza sativa L. ssp. japonica) of cultivar M202 and its near-isogenic, Sub1 introgression line, M202(Sub1), were sterilized for 30 min in a solution of 5% (v/v) bleach and 0.01% (v/v) Tween-20, rinsed and soaked overnight in DI water. After germinating in covered glass dishes on wet paper towels for 5 d, seedlings were transplanted into 10 cm pots in the greenhouse at a planting density of 20 plants per pot. Plants were grown in the greenhouse for 12 d before beginning the submergence treatment.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from frozen shoot tissue with the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany).
cDNA libraries for each sample were prepared from purified mRNA according to Wang et al. (2011).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Random primed libraries
|
| Data processing |
Library strategy: polyA mRNA-Seq
Base calling and demultiplexing performed with Illumina CASAVA version 1.8. (UC Riverside IIGB Genomics Core)
Adapter sequences were trimmed from reads with Trim Galore (Babraham Bioinformatics)
Reads were aligned to the Oryza sativa cv.Nipponbare genome with Tophat2. Parameters as follows: --mate-inner-dist [adjusted for read length] --mate-std-dev 80 --min-intron-length 50 --library-type fr-unstranded --max-intron-length 3000 --max-multihits 1 --coverage-search --segment-mismatches 1 --min-segment-intron 50 --max-segment-intron 3000
Separate .bam alignment files for each sample (6 per sample) were combined and sorted using samtools
Aligned reads per gene were counted for each sample with HTSeq-count. Parameters as follows: -s reverse -m intersection-strict -t gene -i ID
Genome_build: Oryza_sativa.IRGSP-1.0.30
Supplementary_files_format_and_content: Spreadsheet (read_counts_ALocke.xls) with H-Seq-count output for every sample. Gene ID in rows, Sample ID in columns.
|
| |
|
| Submission date |
Aug 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Anna Locke |
| Organization name |
USDA-ARS
|
| Street address |
4112 Williams Hall, 101 Derieux Place
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27695-7620 |
| Country |
USA |
| |
|
| Platform ID |
GPL18525 |
| Series (1) |
| GSE102494 |
mRNA sequencing of whole 15 d old Oryza sativa shoots |
|
| Relations |
| BioSample |
SAMN07490660 |
| SRA |
SRX3085982 |
