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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 01, 2018 |
| Title |
Control tomato fruit Tomato-CTRL_5D_01 |
| Sample type |
SRA |
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| Source name |
tomato fruit
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| Organism |
Solanum lycopersicum |
| Characteristics |
sound treatment: No
sound frequency: NA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using an RNeasy Mini Kit (Qiagen, CA, USA) according to the manufacturer’s protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
The sequencing library was prepared using a TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocol. In brief, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented and converted into cDNA. After the ligation of adapters, the fragments were amplified by PCR.
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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 |
Base calling was performed by Illumina Genome Studio(V2010.1).
Reference genome sequence data for Solanum lycopersicum (tomato) were obtained from the National Center for Biotechnology Information (NCBI) genome database (assembly ID: SL2.50).
STAR was applied to tissue samples for mapping and to quantify reads to the reference genome (ver. 2.5).To estimate gene expression levels, counts per million (CPM) mapped reads values were calculated for each sample. The CPM data were normalised using quantile normalisation in the R language environment (version 3.2.5).
Genome_build: SL2.50
Supplementary_files_format_and_content: tab-delimited text format with log2 transformed CPM values of genes
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| Submission date |
Oct 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Seon-Kyu Kim |
| E-mail(s) |
seonkyu@kribb.re.kr
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| Phone |
+82-42-879-8107
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| Organization name |
Korea Research Institutue of Bioscience & Biotechnology
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| Department |
Personalized Genomic Medicine Research Center
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| Street address |
125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea
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| City |
Daejeon |
| ZIP/Postal code |
305-806 |
| Country |
South Korea |
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| Platform ID |
GPL16345 |
| Series (1) |
| GSE106337 |
Exploring the sound-modulated delay in tomato ripening through expression analysis of RNA. |
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| Relations |
| BioSample |
SAMN07949245 |
| SRA |
SRX3343363 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2836238_Tomato.CTRL_5D_01_log2_CPM.txt.gz |
343.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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