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| Status |
Public on Sep 05, 2023 |
| Title |
orange-derived microRNAs |
| Sample type |
SRA |
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| Source name |
edible portion
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| Organism |
Citrus sinensis |
| Characteristics |
tissue: edible portion
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| Extracted molecule |
total RNA |
| Extraction protocol |
0.1 of fruits (apple, olive, orange, pear, tomato), 0.1 of vegetables (spinach) and 0.5 g of nuts (almond and nut) were ground in QIAzol Lysis Reagent for 1 min using Ultra-Turrax T25 Basic (Basic IKA- WerkeTotal RNA). Total RNA was isolated with miRNeasy Serum/Plasma Kit (Qiagen) according to manufacturer protocol.
Libraries were prepared using the NEBNext® Small RNA Library Prep Set for Illumina kit
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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 |
Adapter were removed from data using skewer.
Read with a size ranging from 15 to 30 bases were aligned to the reference genome with microRNA annotation from miRBase (maximum 2 mismatches in the seed area) using ShortStack.
Mapped tags were counted using htseq-count.
Reads were normalized with DESeq2.
Assembly: Prunus Persica (NCBIv2 and annotation NCBIv2.52 restricted to microRNAs)
Supplementary files format and content: text files that include raw counts for each sample
Supplementary files format and content: text file that includes normalized counts for each Sample
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| Submission date |
Jun 13, 2023 |
| Last update date |
Sep 05, 2023 |
| Contact name |
FermÃn Ignacio Milagro Yoldi |
| E-mail(s) |
fmilagro@unav.es
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| Organization name |
University of Navarra
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| Department |
Department of Nutrition, Food Science and Physiology/Center for Nutrition Research
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| Street address |
C/Irunlarrea,1
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| City |
Pamplona |
| State/province |
Navarra |
| ZIP/Postal code |
31008 |
| Country |
Spain |
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| Platform ID |
GPL21082 |
| Series (1) |
| GSE234786 |
Detection of plant microRNAs in edible-plant based products |
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| Relations |
| BioSample |
SAMN35722468 |
| SRA |
SRX20667117 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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