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| Status |
Public on Apr 02, 2020 |
| Title |
MC_C_2 |
| Sample type |
SRA |
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| Source name |
Pericarp
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| 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
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| Treatment protocol |
Grafted or not; 1.7mM silicon added or not
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Description |
3225 rootstock has strong silicon absorption ability
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| 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
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| Submission date |
Apr 01, 2016 |
| Last update date |
Apr 02, 2020 |
| Contact name |
Zhao Sheng |
| E-mail(s) |
zhaomailcn@126.com
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| Phone |
086-13665368744
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| Organization name |
Shandong Agricultural University
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| Department |
College of Horticultural Science and Engineering
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| Lab |
Vegetables and soilless cultivation
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| Street address |
No.61 Daizong street
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| City |
Tai'an |
| State/province |
Shandong |
| ZIP/Postal code |
271018 |
| Country |
China |
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| Platform ID |
GPL21686 |
| Series (1) |
| GSE79829 |
Grafting changed silicon metabolism and expression of bloom-forming related genes of cucumber pericarp |
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| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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