|
| Status |
Public on Feb 18, 2016 |
| Title |
Stirling 24 h |
| Sample type |
SRA |
| |
|
| Source name |
Germinating seeds
|
| Organism |
Hordeum vulgare subsp. vulgare |
| Characteristics |
varieties: Stirling
|
| Growth protocol |
Seed germinating at 21 oC in dark
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and mRNA was isolated by oligodT column as described by manufactory
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Stirling 24h
|
| Data processing |
Raw sequencing reads were filtered to clean dirty reads and aligned to reference sequences (Mayer et al., 2012) by using SOAPaligner/SOAP2 (Li et al., 2009)
The transcript levels were expressed by reads per kilo base transcriptome per million mapped reads (RPKM)
SOAPsplice software was used for alternative splicing analysis (read 1 mate-pairs only).
Reference genome used: ASM32608v1
Supplementary_files_format_and_content: Barley_Embryo_RNA_seq_Processed.xlsx includes transcript levels (RPKM) values for each Sample
Supplementary_files_format_and_content: BarleySeqMergedForAS.fa: Used for mapping alternative splicing sites on the sequences
|
| |
|
| Submission date |
Feb 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Qisen Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Australian Export Grain Innovation Center
|
| Street address |
3 naron Hay Court
|
| City |
South Perth |
| State/province |
WA |
| ZIP/Postal code |
6151 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19798 |
| Series (1) |
| GSE66024 |
Next generation sequencing reveals gene transcription activities and alternative splicing events in germinating barley embryos |
|
| Relations |
| BioSample |
SAMN03352295 |
| SRA |
SRX882899 |
