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| Status |
Public on Dec 01, 2016 |
| Title |
YL2 rep1 |
| Sample type |
SRA |
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| Source name |
fruit mesocarp
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| Organism |
Prunus persica |
| Characteristics |
tissue: fruit mesocarp
aromatic strength: strong
flesh texture: soft melting
brix: 14.9
cultivar: Yu Lu
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA for each sample was isolated from 1g frozen fruit tissue, according to Zhang (2010). Contaminating genome DNA was removed by RNase-free DNase I (Fermentas, Vilnius, Lithuania). RNA integration and quantification was by agarose electrophoresis at an absorbance of 260nm (A260) using the NanoDrop® ND-3300 Fluorospectrometer with Quant-iT™ RiboGreen® RNA Reagent (Invitrogen, USA). First-strand cDNA was synthesized using 2.0 μl DNA-free RNA with the PrimeScript RT reagent Kit with gDNA Eraser, following the manufacturer’s instructions (Takara), and was diluted for RT-qPCR using a CFX 96 real-time PCR detection system (Bio-Rad, Hercules, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
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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 |
Raw data of fastq format were processed through in-house Perl scripts to obtain clean data by removing reads containing adapter or ploy-N and low quality reads.
Reference genome and gene model annotation files were downloaded from the genome website (http://www.rosaceae.org/species/prunus_persica/genome_v1.0) directly. The index of the reference genome was built using Bowtie v0.12.8, and paired-end clean reads were aligned to the reference genome using TopHat v1.4.0. We selected TopHat as the mapping tool as it can generate a database of splice junctions based on the gene model annotation file, so giving better mapping results than other non-splice mapping tools (Trapnell et al. 2009).
HTSeq v0.5.3 was used to count the reads mapped to each gene, and the RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis of two biological replicates per sample was performed using the DESeq R package (1.10.1) (Wang et al. 2010; Robinson et al. 2010). The P values were adjusted using the Benjamini & Hochberg method (Robinson et al. 2010; Benjamini et al. 1995)
Genome_build: Prunus persica Whole Genome v1.0 Assembly & Annotation
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Dec 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiong-wei Li |
| E-mail(s) |
lixiongweisea@163.com
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| Organization name |
Zhejiang University
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| Department |
Department of Horticulture
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| Street address |
Yuhangtang Road866
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL15671 |
| Series (1) |
| GSE64565 |
Identification of Volatile and Softening-Related Genes Using Digital Gene Expression Profiles in Peach |
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| Relations |
| BioSample |
SAMN03273855 |
| SRA |
SRX825456 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1574417_YL2_rep1_RPKM.txt.gz |
162.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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