 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 27, 2018 |
| Title |
NaSi rep2 |
| Sample type |
SRA |
| |
|
| Source name |
leaves
|
| Organism |
Cucumis sativus |
| Characteristics |
cultivar: JinYou 1
tissue: leaves
condition: salt and silicon treated
|
| Treatment protocol |
Seven days after transplanting, silicon (0.3 mM) and salt (75 mM) treatment were started by adding sodium silicate (Na2SiO3·9H2O) and sodium chloride (NaCl) to the nutrient solution. There were four treatments: control (CT), silicon treatment (Si), salt stress (NaCl), and salt stress plus silicon (NaSi). The pH of nutrient solution was adjusted to 6.0 using 0.2 M H2SO4 or 1 M KOH. Three days after salt and silicon treatment, the recently fully expanded leaves were collected with every 3 of them being mixed as one biological replicate for each treatment. Every treatment had 3 biological replicates, except silicon treatment alone, which had 2 replicates.
|
| Growth protocol |
Cucumber (Cucumis sativus L. ‘JinYou 1’) seeds were rinsed thoroughly in distilled water and germinated on moist gauze in an incubator at 28 °C for 2 days. The germinated seeds were sown in quartz sands in a greenhouse with a day/night temperature of 28℃/18℃. The seedlings were transferred to 15-L plastic containers filled with 1/4 strength of modified Hoagland nutrient solution at two-leaf stage. Three days later, the strength of Hoagland solution was increased to 1/2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using Trizol reagent following manufacture`s protocol (Roche, Mannheim, Germany).
RNA-Seq library construction and sequencing were conducted by Gene Denovo Co. (Guangzhou, China). The poly(A)-containing mRNA molecules were purified from 10 mg of total RNA using poly-T oligo-attached magnetic beads. The extracted mRNAs were fragmented into 200-bp-long pieces using RNA Fragmentation Buffer (Kapa, Biosystems). The cleaved Illumina Sequencing mRNA fragments were reverse-transcripted into first-strand cDNA using random primers, followed by second-strand cDNA synthesis using DNA Polymerase I and RNase H. Then, the cDNA fragments went through an end repair process, the addition of a single “A” base, and ligation of the adapter sequences. Finally, the cDNA products were purified and enriched to construct libraries for non-strand-specific RNA-Seq.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Cucumber leaves from salt and silicon treated seedlings
|
| Data processing |
Sequenced clean reads were mapped to cucumber genome (v2) using TopHat2 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated according to the protocol (Trapnell et al., Nature protocols, 2012).
Genome_build: GCF_000004075.2
Supplementary_files_format_and_content: txt files showing the RPKM values of genes for each Sample
|
| |
|
| Submission date |
Jun 26, 2018 |
| Last update date |
Jun 27, 2018 |
| Contact name |
Ruolin Yang |
| E-mail(s) |
desert.ruolin@gmail.com
|
| Organization name |
Northwest A&F University
|
| Street address |
No.3 Taicheng Road
|
| City |
Yangling |
| State/province |
Shaanxi |
| ZIP/Postal code |
712100 |
| Country |
China |
| |
|
| Platform ID |
GPL20825 |
| Series (1) |
| GSE116265 |
Transcriptomic dynamics provides an insight into the mechanism for silicon-mediated alleviation of salt stress in cucumber plants |
|
| Relations |
| BioSample |
SAMN09487595 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3223388_NaSi-rep2.RPKM.xlsx.gz |
446.1 Kb |
(ftp)(http) |
XLSX |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
