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Sample GSM3946117 Query DataSets for GSM3946117
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
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
 
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

Supplementary file Size Download File type/resource
GSM3946117_Cn_XS_0_1A.gene.FPKM.txt.gz 264.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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