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Sample GSM3176788 Query DataSets for GSM3176788
Status Public on Jun 11, 2018
Title seeds following 2 d of aerobic germination (2dA) Replicate 1
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 1
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 SAMN09371481
SRA SRX4169495

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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