|
| Status |
Public on Jun 11, 2018 |
| Title |
seeds following 2 d of aerobic germination (2dA) Replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Rice coleoptile
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: coleoptile
genotype: WT(Oryza sativa cv Amaroo)
age: seeds following 2 d of aerobic germination (2dA) Replicate 3
treatment/conditions: De-hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30 C in the dark for 2 d.
|
| Treatment protocol |
For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
|
| Growth protocol |
Rice (Oryza sativa ‘Amaroo’) was de‐hulled, surface sterilised and grown in culture medium [0.5 mm 2‐(N‐morpholine)‐ethanesulphonic acid (MES), 0.4 mm CaSO4, pH 6.5) that was bubbled with air or nitrogen gas (N2) (6–7 L min−1).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was carried out using the Sigma Spectrum Plant Total RNA kit.
TruSeq Stranded Total RNA with Ribo‐Zero Plant Sample Prep Kits were used to generate the libraries, according to manufacturer’s instructions (Illumina).
rRNAs removed, random fragmentation, stranded library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
De‐hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30°C in the dark for 2 d, coleoptiles were immediately extracted and snap frozen.
|
| Data processing |
Quality control was confirmed within the Illumina Hiseq software and all reads passing filter were used for downstream analysis.
Filtered reads were mapped onto O.sativa genome with the International Rice Genome Sequencing Project 1.0 (IRGSP‐1.0) rice genome sequence (from the RAP‐DB). The cufflinks package (Trapnell et al., 2012) version 2.2.0 (Bowtie2 v.2.2.0‐beta7 and Tophat v.2.2.0) was used for RNA‐seq analyses.
Genome_build: International Rice Genome Sequencing Project 1.0 (IRGSP‐1.0) and MSU v.7
Supplementary_files_format_and_content: tab-delimited text files showing results from differential expression analyses using Cuffdiff (v. 2.2.0).
|
| |
|
| Submission date |
Jun 05, 2018 |
| Last update date |
Jun 11, 2018 |
| Contact name |
Reena Narsai |
| Organization name |
La trobe University
|
| Street address |
5 Ring road
|
| City |
Bundoora |
| ZIP/Postal code |
3083 |
| Country |
Australia |
| |
|
| Platform ID |
GPL25149 |
| Series (2) |
| GSE115371 |
RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq) |
| GSE115373 |
RNA-seq and DNA methylomes of germinating rice and developing coleoptiles |
|
| Relations |
| BioSample |
SAMN09371479 |
| SRA |
SRX4169497 |
