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Status |
Public on Nov 28, 2015 |
Title |
ow-0DPAe RNA-seq R06_rep2 |
Sample type |
SRA |
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Source name |
ovary wall/pericarp of 0DPAe (emasculated) fruit
|
Organism |
Solanum lycopersicum |
Characteristics |
tissue: ovary wall/pericarp Stage: 0DPA (emasculated at -2DPA)
|
Treatment protocol |
No treatment
|
Growth protocol |
the tomato plants were grown in greenhouse on soil
|
Extracted molecule |
total RNA |
Extraction protocol |
the fruits of different stages were collected and the ovule and ovary wall were dissected under microscope. The total RNA was extracted using TRIZOL reagent (Invitrogen Cat#15596026). Strand-specific RNA-Seq libraries generated from samples above were constructed using dUTP method (Parkhomchuk et al., 2009) and sequenced on Illumina Hiseq 2500.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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|
Data processing |
The RNA-seq reads were aligned to the tomato genome (ITAG2.4) using tophat-2.0.11 (Trapnell et al., 2009) with anchor length more than 8nt for spliced alignments. Only uniquely mapped reads were retained for subsequent analysis. Genome_build: ITAG2.4 Supplementary_files_format_and_content: bigWig
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Submission date |
Aug 19, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Lianfeng Gu |
Organization name |
Fujian Agriculture and Forestry University
|
Street address |
No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China
|
City |
fuzhou |
ZIP/Postal code |
350002 |
Country |
China |
|
|
Platform ID |
GPL19694 |
Series (1) |
GSE72216 |
Spatial-temporal order of regulation in tomato early fruit development |
|
Relations |
BioSample |
SAMN04002496 |
SRA |
SRX1160120 |