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Sample GSM6123278 Query DataSets for GSM6123278
Status Public on Jun 01, 2023
Title 27p
Sample type SRA
 
Source name equine lung tissue
Organism Equus caballus
Characteristics tissue: lung tissue
molecule subtype: microRNA
Treatment protocol Immediately after slaughter, tissue samples were put in RNA Later solution (Thermo Fisher Scientific) and stored at -80°C
Extracted molecule total RNA
Extraction protocol The quantity and quality of the obtained RNA were checked on a NanoDrop 2000 spectrophotometer (Thermo Scientific; Wilmington, USA) and on a TapeStation 2200 instrument (RNAScreen Tape, Agilent, Perlan Technologies, Poland).
microRNA libraries were prepared with the use of NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs; E7300L), according the standard protocol. Briefly, the first step was the 3’ adaptor ligation, followed by hybridization with the Reverse Transcription Primer and ligation with the 5’ adaptor. The RNA-adaptor ligation products were subjected to reverse transcription. Then, PCR amplification with 12 different indexed primers was performed to allow further multiplexing of the samples. The amplified samples were purified and size-selected on a Novex 6% TBE PAGE gel (Invitrogen). After the overnight elution from the gel, the libraries were precipitated and purified with ethanol (POCH). Next, they were subjected to a concentration measurement with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and a size assessment with a 2200 TapeStation instrument (Agilent). The libraries were stored at -20°C at 10nM concentration until further use.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
 
Data processing demultiplexing: bcl2fastq
quality control: FastQC
trimming off the 3' adapter sequences and length filtering (18-26 nt): Trimmomatic, Flexbar
mapping: the filtered reads were mapped to EcuCab3.0 genome using BWA
miRNA identification: miRDeep2 with default parameters with reference to miRBAse 22.1
differential expression analysis: DESeq2 (a Bioconductor R-project package)
Assembly: EcuCab3.0
Supplementary files format and content: CSV file with normalized abundance measurments for all investigated samples
 
Submission date May 09, 2022
Last update date Jun 01, 2023
Contact name Klaudia Pawlina-Tyszko
E-mail(s) klaudia.pawlina@iz.edu.pl
Organization name National Research Institute of Animal Production
Department Deaprtment of Animal Genomics and Molecular Biology
Lab Laboratory of Genomics
Street address Krakowska 1
City Balice near Krakow
ZIP/Postal code 32-083
Country Poland
 
Platform ID GPL21401
Series (1)
GSE202502 Equine tissue miRNA profiling
Relations
BioSample SAMN28159190
SRA SRX15208548

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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