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Sample GSM2836238 Query DataSets for GSM2836238
Status Public on Nov 01, 2018
Title Control tomato fruit Tomato-CTRL_5D_01
Sample type SRA
 
Source name tomato fruit
Organism Solanum lycopersicum
Characteristics sound treatment: No
sound frequency: NA
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
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
 
Submission date Oct 30, 2017
Last update date May 15, 2019
Contact name Seon-Kyu Kim
E-mail(s) seonkyu@kribb.re.kr
Phone +82-42-879-8107
Organization name Korea Research Institutue of Bioscience & Biotechnology
Department Personalized Genomic Medicine Research Center
Street address 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea
City Daejeon
ZIP/Postal code 305-806
Country South Korea
 
Platform ID GPL16345
Series (1)
GSE106337 Exploring the sound-modulated delay in tomato ripening through expression analysis of RNA.
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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