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Sample GSM1133799

Query DataSets for GSM1133799

Status

Public on May 07, 2015

Title

root LN

Sample type

SRA

Source name

cucumber root

Organism

Cucumis sativus

Characteristics

age: 28-day after sowing
tissue: root
treatment: low nitrogen

Treatment protocol

At the low N stress condition (LN), plants were fed a 1 mM nitrogen solution (0.8 mM KNO3, 0.1 mM Ca(NO3)2,0.25 mM KH2PO4, 0.25 mM MgSO4,1.2 mM K2SO4, 0.8 mM KCl,0.4 mM CaCl2, 0.2 mM NaCl). Control plants (CK)were fed a complete nutrient solution containing 5 mM nitrate as nitrogen source (4 mM KNO3, 0.5 mM Ca(NO3)2, 0.25 mM MgSO4, 0.25 mM KH2PO4, 0.2 mM NaCl). All nutrient solutions contained oligoelements (24 μM H3BO3, 10 μM MnSO4, 3 μM ZnSO4, 0.9 μM CuSO4, 0.04 μM (NH4)6Mo7O24), and iron-EDTA 10 mg /L

Growth protocol

cucumber seeds were germinated and grown in plastic pots containing clean sand. Plants were grown in a growth chamber under a 14/10h photoperiod at 25℃(day)and 18℃(night), and 65% humidity.

Extracted molecule

total RNA

Extraction protocol

roots and leaves from plants of CK and LN were taken, a total of 0.1g tissue for each sample was frozen in liquid nitrogen and stored at -80℃ prior to use,and RNA was harvested using Trizol reagent. Illumina Gene Expression Sample Prep Kit was used with 6 ug of total RNA for the construction of sequencing libraries.
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

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, then mapped to Cucumis sativus L. whole genome using bowtie v0.12.9 with parameters -t -k 2 -v 1 -p 16 --sam --quiet --solexa-quals --chunkmbs 256 --sam-nohead --sam-nosq --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol of in house. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Cucumis sativus L. v1.0/CucSat_1.0
Supplementary_files_format_and_content: he reads and RPKM number for each expressed genes of cucumber ,and for all samples (phytozome at JGI)

Submission date

May 06, 2013

Last update date

May 15, 2019

Contact name

Dong Chen

E-mail(s)

[email protected]

Organization name

Nissi Biotech

Street address

888 Gaoxin Avenue