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| Status |
Public on Jun 01, 2023 |
| Title |
30p |
| Sample type |
SRA |
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| Source name |
equine lung tissue
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| Organism |
Equus caballus |
| Characteristics |
tissue: lung tissue
molecule subtype: microRNA
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| Treatment protocol |
Immediately after slaughter, tissue samples were put in RNA Later solution (Thermo Fisher Scientific) and stored at -80°C
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| 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.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
May 09, 2022 |
| Last update date |
Jun 01, 2023 |
| Contact name |
Klaudia Pawlina-Tyszko |
| E-mail(s) |
klaudia.pawlina@iz.edu.pl
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| Organization name |
National Research Institute of Animal Production
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| Department |
Deaprtment of Animal Genomics and Molecular Biology
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| Lab |
Laboratory of Genomics
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| Street address |
Krakowska 1
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| City |
Balice near Krakow |
| ZIP/Postal code |
32-083 |
| Country |
Poland |
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| Platform ID |
GPL21401 |
| Series (1) |
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| Relations |
| BioSample |
SAMN28159187 |
| SRA |
SRX15208551 |
| 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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