|
Status |
Public on Apr 10, 2017 |
Title |
M82 54 DPA rep1 |
Sample type |
SRA |
|
|
Source name |
M82 54 DPA_fruit pericarps
|
Organism |
Solanum lycopersicum |
Characteristics |
cultivar background: M82 developmental stage: 54 DPA genotype/variation: Wild Type phentoype: red-fruited tomato tissue: fruit pericarps
|
Growth protocol |
Plants were grown in a greenhouse at at Pujiang experimental base, Shanghai Jiao Tong University, Shanghai, China.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted using RNAprep pure Plant Kit (Cat#DP441). Sequencing libraries were constructed using Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001). RNA libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Illumina Casava software used for basecalling. Raw reads were screened by FASTX-Toolkit to remove adaptor sequences and low-quality regions. The remaining high-quality reads were mapped to tomato reference genome (ITAG2.3) using TopHat (version 2.0) fragments per kilobase of exon per million fragments mapped (FPKM) calculated by Cufflinks (http://cufflinks.cbcb.umd.edu/). Genome_build: Solanum lycopersicum reference genome (ITAG2.3); http://www.ncbi.nlm.nih.gov/assembly/GCF_000188115.2 Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample in each pairwise comparison (the gene locus can be traceable in Sol Genomics Network (https://solgenomics.net/search/locus)
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|
|
Submission date |
Oct 10, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Lei Gao |
E-mail(s) |
glei1103@hotmail.com
|
Organization name |
Shanghai Jiao Tong University
|
Street address |
Dongchuan Road No. 800
|
City |
Shanghai |
ZIP/Postal code |
200240 |
Country |
China |
|
|
Platform ID |
GPL16345 |
Series (1) |
GSE73908 |
Transcriptomic difference between the wild type red-fruited tomato and its yellow-fruited mutant |
|
Relations |
BioSample |
SAMN04159006 |
SRA |
SRX1326492 |