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Sample GSM4238144 Query DataSets for GSM4238144
Status Public on Apr 13, 2020
Title WT rep2
Sample type SRA
 
Source name Ailsa Craig
Organism Solanum lycopersicum
Characteristics developmental stage: At 37 days after anthesis (dpa)
tissue: Pericarp
genotype: wild type (WT)
Growth protocol Wild-type tomato and transgenic lines in the Ailsa-Craig background were grown in a greenhouse at 23°C under 16 h light and 8 h dark condition.
Extracted molecule total RNA
Extraction protocol Pericarp tissues were collected, immediately frozen in liquid nitrogen, and total RNA was extracted using Trizol reagent kit. mRNA Seq Kit (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Illumina Casava1.7 software used for basecalling.
Raw reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the tomato reference genome (version SL3.0) using HISAT2.2.4 with "-rna-strandness RF" and other parameters set as a default.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Tomato reference genome (version SL3.0)
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample
 
Submission date Dec 30, 2019
Last update date Apr 13, 2020
Contact name Li Zhiwei
E-mail(s) lizhiwei@scbg.ac.cn
Phone 18825179606
Organization name South China Botanical Garden, Chinese Academy of Sciences
Lab Key Laboratory of Plant Resources Conservation and Sustainable Utilization
Street address No.723,Xingke Road
City Guangzhou
ZIP/Postal code 518000
Country China
 
Platform ID GPL25655
Series (2)
GSE142713 Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato [RNA-Seq]
GSE142714 Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato
Relations
BioSample SAMN13698532
SRA SRX7477123

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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