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Sample GSM2304573

Query DataSets for GSM2304573

Status

Public on Sep 02, 2019

Title

WT-fruit-2

Sample type

SRA

Source name

WT-fruit

Organism

Cucumis sativus

Characteristics

genotype background: inbred line 1461
genotype/variation: wild type
tissue: fruit

Growth protocol

Cucumber (Cucumis stativus L.) inbred line R1461, a northern China type cucumber with dark green fruits similar to the sequenced Chinese Long 9930, was used in this study. The cucumber seeds were germinated in 28℃ in dark, and grown in a growth chamber under 16h/8h and 25ºC/18ºC in day/night until two true-leaf stage, then the cucumber seedlings were transferred to a greenhouse under standard conditions in the experimental field of China Agricultural University in Beijing. Water management and pest control were performed according to standard protocols. The Arabidopsis seeds of ind-2 mutant were obtained from Lars Østergaard (Girin et al., 2011). The Arabidopsis thaliana Columbia (Col) ecotype and ind-2 plants were grown in soil in a growth chamber under 16h light/8h dark at 22℃.

Extracted molecule

total RNA

Extraction protocol

Leaf veins and fruits four days before anthesis of WT and transgenic cucumber plants were collected for RNA-seq analysis. Total RNAs were extracted using the RNA extraction kit (Huayueyang, Beijing, China), and RNA quality check were performed as previously described (Sun et al., 2016). Two biological replicates were performed for each tissue sample. RNA-seq library construction was performed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA) according to the manufacturer’s instructions and four index codes were added to attribute sequences to different samples(Wang et al., 2009).
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.
Please note that [1] the identifiers in the processed data file is searchable at: http://www.icugi.org/cgi-bin/ICuGI/genome/home.cgi?ver=2&organism=cucumber&cultivar=Chinese-long [2] the "M" is changed to "G", and the isoform information has been deleted. For example, the "Csa3G002400" correponds to "Csa3M002400.1" in the website.
Genome_build: v2i (http://cucumber.genomics.org.cn)
Supplementary_files_format_and_content: Tab-delimited text file include RPM(Reads per Million) values for 8 Samples .

Submission date

Sep 06, 2016

Last update date

Sep 02, 2019

Contact name

Hailing Zi

E-mail(s)

[email protected]

Organization name

Shanghai center for plant stress biology

Street address

Chenhua road3888