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Sample GSM3076087

Query DataSets for GSM3076087

Status

Public on Dec 01, 2018

Title

2: Flesh-3d

Sample type

SRA

Source name

Flesh of the cucumber inbred line ‘YB’ at 3 days after slef-pollination

Organism

Cucumis sativus

Characteristics

line: YB
tissue: Flesh
developmental stage: 3 days after slef-pollination

Treatment protocol

For RNA-Seq, the peels and flesh of 'YB' at 3, 6, 9d of pollination were used and each sample were mixed by 3 fruits.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using RNAiso Plus Total RNA extraction reagent (Cat#9109, TAKARA, China) and a RNeasy Mini Kit (Cat#74106, Qiagen) following the manufacturer’s instructions, the RIN number was subsequently determined to evaluate RNA integrity using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).
Qualified total RNA was further purified using a RNeasy Micro Kit (Cat#74004, QIAGEN, GmBH, Germany) and a RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany). The purified total RNA was then subjected to mRNA isolation, removal of rRNA, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, terminal repair, 3' end addition of an ‘A’, ligation and enrichment. Finally, sample libraries were constructed. The nucleic acid concentrations of the libraries were measured using a Qubit® 2.0 Fluorometer, and the Agilent 2100 system was used to determine the size of the library.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome（version:ATCC 35984）using TopHat（version:2.0.9).
Cufflinks v2.1.1 was used to count the read numbers mapped to each gene
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: cucumber Chinese long genome v2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

Submission date

Apr 04, 2018

Last update date

Dec 01, 2018

Contact name

Xuewen Xu

E-mail(s)

596620842@qq.com

Organization name

Yangzhou University

Street address

48 wenhui east road