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| Status |
Public on Jun 25, 2018 |
| Title |
Coconut |
| Sample type |
SRA |
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| Source name |
Exosome-like nanoparticles
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| Organism |
Cocos nucifera |
| Characteristics |
tissue: Coconut fruit
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| Treatment protocol |
First, the peel of edible plants with more Juice was cut away, then the fleshes were wrapped with gauze and squeezed by hand, while less Juice of edible plants with PBS were ground in a mixer to obtain the juice. Subsequently, the collected juice was sequentially centrifuged at 1,200g for 20 min, 3,000g for 20 min, and followed by centrifugation (10,000g , 60 min, 4°C) in a Sorvall Lynx 6000 (Fisher Scientific) to remove large particles and cellular debris. Afterwards, it was filtered through filtrator of 1μm (Millipore Corp., Bedford, MA), and the supernatant was centrifuged at 150,000 × g for 90 min at 4 °C in a LE-80 ultracentrifuge (Beckman Coulter; Palo Alto, CA) to pellet EPDELNs, the final fraction was resuspended in 250ul of PBS.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was harvested using Trizol-LS reagent.
The integrity of total RNA was determined by the Agilent 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit with suitable RNA samples having an RNA integrity number > 6.5. Approximately, 15 μg of small RNA-enriched total RNA was prepared for high-throughput sequencing. For each library, small RNA ranging from 15 to 35 nt was purified by 15% Tris-bora-EDTA polyacrylamide gel electrophoresis, and 3´ and 5´ adaptors were ligated with unique small RNA fractions. The modified small RNA was then reverse-transcribed and amplified by reverse transcription-PCR. Finally, the enriched cDNA was sequenced on a Illumina HiSeq 2500 according to the manufacturer’s instructions.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
microRNA
miRNA-derived exosome-like nanoparticles in Coconut.
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| Data processing |
Original sequence was subjected to a series of stringent filters (such as removing low quality reads, repeated sequences and adaptor sequences) and called clean data.
The filtered reads were identified by matching with all known plant mature miRNAs deposited in the miRBase21.0 (November 2016) database (http://www.mirbase.org/index.shtml) with no more than 2 mismatch.
For each sample, counts were first normalized by the total count of mappable reads which is denoted as reads per million (RPM).
Supplementary_files_format_and_content: *.txt: Tab-delimited text files; Identified miRNAs in each library with count reads and normalized data.
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| Submission date |
Jun 20, 2018 |
| Last update date |
Feb 07, 2019 |
| Contact name |
Juan Xiao |
| E-mail(s) |
XiaoJuan751190178@163.com
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| Phone |
18283582445
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| Organization name |
Sichuan Agricultural University
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| Department |
Institute of Animal Genetics and Breeding, College of Animal Science and Technology
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| Lab |
The Laboratory of swine
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| Street address |
Huimin road No.211, Wenjiang
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| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
611130 |
| Country |
China |
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| Platform ID |
GPL25220 |
| Series (1) |
| GSE116095 |
Identification of Exosome-Like Nanoparticle Derived MicroRNAs from Eleven Edible Plants |
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| Relations |
| BioSample |
SAMN09466645 |
| SRA |
SRX4278022 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3208888_Coconut.txt.gz |
1.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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