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Status |
Public on Mar 30, 2020 |
Title |
T5-3 |
Sample type |
SRA |
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Source name |
Ovary tissue
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Organism |
Cucumis sativus |
Characteristics |
tissue: Ovary time: the embryos were cultured for 60d
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA was isolated using TRIzol (Invitrogen), and DNase I (Fermentas) digestion was performed for 30 min at 25 oC to remove DNA, according to the manufacturer’s instructions. The integrity and quality of the total RNA were checked using a NanoDrop 1000 spectrophotometer and formaldehyde-agarose gel electrophoresis. RNA was used only when the OD260: OD280 ratio was above 1.8. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina HiSeqTM 2000 at the (Personal-bio, China) following the vendor's recommended protocol. RNA libraries were prepared for sequencing using standard Illumina protocols
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Data processing |
Illumina HiSeq 2000 software used for basecalling. The reads with more than 10% unknown bases and those of low quality were removed from the raw sequencing data using the software Illumina GA Pipeline (v1.6). The filtered reads were aligned to the cucumber Chinese long v2 genome using TopHat2 (http://tophat.cbcb.umd.edu/) software. Use HTSeq 0.6.1p2 (http://www-huber.embl.de/users/anders/HTSeq) to compare the read count value of each gene as the original expression amount of the gene perform expression level for mRNAs by calculating RPKM Genome_build: Cucumis_sativus_v 20 Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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Submission date |
Mar 20, 2020 |
Last update date |
Mar 30, 2020 |
Contact name |
LU YUXI |
E-mail(s) |
lyxrun@sina.com
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Organization name |
Institute of Horticulture
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Street address |
Guizhou Academy of Agricultural Sciences
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City |
Guiyang |
ZIP/Postal code |
55006 |
Country |
China |
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Platform ID |
GPL16310 |
Series (1) |
GSE147282 |
Analysis of transcriptomic regulation mechanisms underlying cucumber (Cucumis sativus L.) embryogenesis during ovary culture |
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Relations |
BioSample |
SAMN14414646 |
SRA |
SRX7959769 |
Supplementary data files not provided |
SRA Run Selector![Help](/coreweb/images/long_help4.gif) |
Raw data are available in SRA |
Processed data are available on Series record |
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