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Sample GSM2104395 Query DataSets for GSM2104395
Status Public on Apr 02, 2020
Title MC_C_2
Sample type SRA
 
Source name Pericarp
Organism Cucumis sativus
Characteristics code name: C/M2-
grafted or not: cucumber grafted onto "3225" pumpkin rootstock
treatment: cultivated by deionized water nutrient solution
phenotype: With sparse bloom
Treatment protocol Grafted or not; 1.7mM silicon added or not
Growth protocol Seedlings were washed clean by tap-water, swathed around root and bottom stem using thin sponge and transplanted into a hole of 3cm thick cystosepiment. We used “Yamazaki cucumber nutrient solution formula” prepared by deionized water (with Si 8.7×10-4mM) as nutrient solution, aerated continuously and refreshed solution every 4~5 days. Other cultural practices adopt cucumber routine management In flowering period, we added potassium silicate to keep the silicon concentrations to 1.7mM and collect pericarp in two hours.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from each tissue using the TRIzol reagent according to the manufacturer’s protocol (Invitrogen, Burlington, ON, Canada). DNA was removed from RNA extracts by incubation with RNase-free DNase(New England Biolabs) for 30 min at 37°C. The RNA integrity and concentration was evaluated using an Agilent Technologies 2100 Bioanalyzer. Each sample had RNA Integrity Number (RIN) values greater than 7.5.
Poly(A) mRNA was isolated from total RNA using oligo(dT) magnetic beads (Invitrogen, Carlsbad, CA, USA). Fragmentation buffer was added to break the purified mRNA into short fragments. Using these short fragments as templates, first-strand cDNA synthesis was performed using random hexamer primers and reverse transcriptase (Invitrogen). Second-strand cDNA was synthesized using RNase H (Invitrogen), DNA polymerase I (New England Biolabs), dNTPs and buffer. Subsequently, the short fragments were purified using the QIAquick PCR extraction kit, eluted with EB buffer and end repaired. Poly(A) tails were added, and the fragments were ligated to sequencing adaptors. We then selected suitable fragments as templates for PCR amplification according to the results of agarose gel electrophoresis. The average insert size for the paired-end libraries was 200 bp (from 180 to 220 bp). Sixteen paired-end cDNA libraries were constructed, one for each sample. Finally, the cDNA libraries were loaded onto the flow cell channels of an Uon Proton platform for paired-end 140 bp×2 sequencing at the Beijing Genomics Institute (BGI), Shenzhen, China.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Description 3225 rootstock has strong silicon absorption ability
Data processing Remove low quality reads, adaptor sequences, or unknown bases (N),which is greater than 10% from raw reads, and obtain “clean reads”
Reads mapping to the cucumber Genome (V2) and Sequencing quality assessment
Assess sequencing, Quantification of gene expression
 Expression pattern analysis of DEGs
Gene ontology enrichment analysis of DEGs
Draw Venn diagram, Go enrichment,and Cluster diagram
Each gene has unique gene ID, which is from cucumber (Cucumis sativus L.) genome (http://www.icugi.org/cgi-bin/ICuGI/genome/index.cgi?organism=cucumber)
Genome_build: cucumber Chinese long genome V2
Supplementary_files_format_and_content: Excel 2003 in GeneDiffExp,GeneDiffExpFilter
 
Submission date Apr 01, 2016
Last update date Apr 02, 2020
Contact name Zhao Sheng
E-mail(s) zhaomailcn@126.com
Phone 086-13665368744
Organization name Shandong Agricultural University
Department College of Horticultural Science and Engineering
Lab Vegetables and soilless cultivation
Street address No.61 Daizong street
City Tai'an
State/province Shandong
ZIP/Postal code 271018
Country China
 
Platform ID GPL21686
Series (1)
GSE79829 Grafting changed silicon metabolism and expression of bloom-forming related genes of cucumber pericarp
Relations
BioSample SAMN04600333
SRA SRX1674696

Supplementary file Size Download File type/resource
GSM2104395_MC_C_2.Gene.rpkm.xls.gz 1.4 Mb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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