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Status |
Public on Jan 19, 2021 |
Title |
Cn_XS_0_1A |
Sample type |
SRA |
|
|
Source name |
Aromatic coconut_0h
|
Organism |
Cocos nucifera |
Characteristics |
cultivar: Aromatic Coconut (XS) time: 0h tissue: leaves
|
Treatment protocol |
A Salt stress experiment was conducted on coconut palms seedlings, weekly irrigated on Murashige and Skoog (MS) culture medium and then enriched with 200 mM NaCl (time 0). After four hours the osmotic stress reached the leaves but not yet the cation stress; after six days the osmotic stress was still present in the leaves and the ionic stress could be felt; at seven days, a second irrigation of MS with 200 mM was performed; after ten days the osmotic and cation stresses should be present in the leaves (after two irrigation there was a NaCl accumulation).Varieties used are Hainan Tall (DB) and Aromatic Coconut (XS).
|
Growth protocol |
The coconut seedling were used the experiments, the seedling is about four to five month old and 50 cm in height in a container located in the greenhouse.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was isolated by modified CTAB methods. RNA libraries were prepared for sequencing using standard Illumina protocols
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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|
Description |
150717_I806_FCC7AVTACXX_L1_WHCOCrqgRAACRAAPEI-33
|
Data processing |
Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences. use BWA (Li, H. and Durbin, R., 2009) to map clean reads to genome reference and use Bowtie (Langmead B, et al., 2009) to gene reference Genes expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). RSEM (Li B and Dewey C N., 2011) Genome_build: CN-sc1 Supplementary_files_format_and_content: RPKM values for each Sample
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|
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Submission date |
Jul 17, 2019 |
Last update date |
Jan 19, 2021 |
Contact name |
Yaodong Yang |
E-mail(s) |
yyang@catas.cn
|
Phone |
008689863330470
|
Organization name |
Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences
|
Street address |
No. 496 Wenqing Av.
|
City |
Wenchang City |
State/province |
Hainan |
ZIP/Postal code |
571339 |
Country |
China |
|
|
Platform ID |
GPL26924 |
Series (1) |
GSE134410 |
Gene expression under high salt stress for coconut |
|
Relations |
SRA |
SRX6456239 |
BioSample |
SAMN12306841 |