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| Status |
Public on Feb 11, 2017 |
| Title |
TBD-623 |
| Sample type |
SRA |
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| Source name |
Peach
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| Organism |
Prunus persica |
| Characteristics |
cultivar: Troubador
development: Sampling at 35, 55, 75, 90, 105 days after full bloom
tissue: Fruit
flesh color: Yellow flesh
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| Treatment protocol |
Collect fruit at 35, 55, 75, 90, 105 days after full bloom,respectively
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| Growth protocol |
Six-year old ‘Troubador’ peach trees grown under standard field conditions at the National Peach Germplasm Repository in Nanjing, China.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the fruit samples using Trizol reagent and subsequently treated with DNaseI (Takara Biotechnology Co., Ltd, Dalian, China) per the manufacturer’s instructions to remove contamination by genomic DNA.
sRNA fractions of 18 to 30 nt in length were first purified from the low-molecular weight RNA by excision from 15% denaturing polyacrylamide gels and then ligated to 3’ and 5’ adaptors using T4 RNA ligase according to the manufacturer’s instructions. The sRNAs ligated with 3’ and 5’ adaptors were purified and reverse transcribed to cDNA with the reverse transcription primers for 17 cycles according to the protocol. Eventually, the PCR products were further purified and subjected to sequencing using the Illumina Genome Analyzer. The image files obtained from the analyzer were then evaluated and used to form a large repertoire of digital data suitable for bioinformatics analysis. Degradome library was constructed following with methods previously described by Ma et al.(2010). CleaveLand3.0 program was used to detect potentially sliced targets of known and novel miRNA.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software
Sequencing image was analyzed by Pipeline Firecrest Module.
Base-calling was done by Pipeline Bustard Module
CleaveLand3.0 was used for alignment, filtering, peak-calling and so on.
Genome_build: http://www.ncbi.nlm.nih.gov/genome/388?genome_assembly_id=28754:assembly Prupe1_0
Supplementary_files_format_and_content: Profiles of Peach miRNAs.xls, miRNA sequence and expression data, Degradome_Targets_prediction.xlsx, miRNA target prediction results,target position and degradome fragments abundance on cleavage position
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| Submission date |
Jun 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
ZHANG chunhua |
| E-mail(s) |
[email protected]
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| Organization name |
Jiangsu Academy of Agricultural Sciences
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| Street address |
Xuanwu road
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| City |
Nanjing |
| ZIP/Postal code |
210014 |
| Country |
China |
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| Platform ID |
GPL21993 |
| Series (1) |
| GSE83110 |
The identification of known and novel microRNAs and their targets in peach (Prunus persica) fruit by high-throughput sequencing |
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| Relations |
| BioSample |
SAMN05214399 |
| SRA |
SRX1830195 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2193136_Summary_of_miRNAs.xlsx |
37.2 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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