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Sample GSM7474766 Query DataSets for GSM7474766
Status Public on Sep 05, 2023
Title almond-derived microRNAs
Sample type SRA
 
Source name edible portion
Organism Prunus dulcis
Characteristics tissue: edible portion
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
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
 
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
 
Submission date Jun 13, 2023
Last update date Sep 05, 2023
Contact name Fermín Ignacio Milagro Yoldi
E-mail(s) fmilagro@unav.es
Organization name University of Navarra
Department Department of Nutrition, Food Science and Physiology/Center for Nutrition Research
Street address C/Irunlarrea,1
City Pamplona
State/province Navarra
ZIP/Postal code 31008
Country Spain
 
Platform ID GPL27530
Series (1)
GSE234786 Detection of plant microRNAs in edible-plant based products
Relations
BioSample SAMN35722471
SRA SRX20667114

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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