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Sample GSM1982084

Query DataSets for GSM1982084

Status

Public on Jul 25, 2016

Title

Super_DAL5.rep3

Sample type

SRA

Source name

corolla

Organism

Cucumis sativus

Characteristics

age: 5DAL
tissue: corolla
genotype: inbred line 6457
phenotype: super ovary bloom

Treatment protocol

This was followed by two kinds of treatments during the full bearing period:(1) super ovary induction treatment, fertilizer and water adequacy , only one fruit (the first female flower near the growing point) was set per plant to limit interfruit competition effects on fruit development and yield super ovary; (2) normal ovary induction treatment, fertilizer and water deficiency, one or two fruits (exceptthe first female flower near the growing point) were set per plant to promote the yield of normal ovary.

Growth protocol

The cucumber inbred line '6457' (parthenocarpic rate≥95%) was grown in a greenhouse with a 12h photoperiod, a mean daily air temperature of 29/20℃(day/night), a relative humidity of 85% and a photosynthetic photo flux density of 800μmolm-2s-1at Hebei Normal University of Science and Technology. Pest control was performed according to standard management practices. The female flowers at the top node of the main stem, were treated prior to bagging in order to prevent pollination.

Extracted molecule

total RNA

Extraction protocol

As described above, 11 kinds of corolla samples were collected for RNA-seq analysis. For each sample, 5 individual corollas were ground into powder and mixed in liquid nitrogen (three replicates). Total RNAs were isolated using the RNA extraction kit (Huayueyang, China). RNA was checked on 1% agarose gels to avoid possible degradation and contamination, and was then examined by a Nano Photometer spectrophotometer (IMPLEN, CA, USA) for RNA purity. Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA) was used to measure RNA concentration, and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) was used to evaluate RNA integrity.
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.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 17 and length >= 25 bp). Clean reads were mapped to the Cucumber genome sequence (http://cucumber.genomics.org.cn, v2i) using TopHat. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed and only genes with an expression level of at least 1 RPM (readss per million) in at least two samples were kept for further analysis.
Genome_build: v2i
Supplementary_files_format_and_content: Tab-delimited text file include RPM (Reads per Million) values for 33 Samples .

Submission date

Dec 28, 2015

Last update date

May 15, 2019

Contact name

Renyi Liu

E-mail(s)

[email protected]

Phone

02157078228

Organization name

Shanghai Center for Plant Stress Biology