 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 17, 2021 |
| Title |
42s |
| Sample type |
SRA |
| |
|
| Source name |
porcine backfat
|
| Organism |
Sus scrofa |
| Characteristics |
diet: cDDGS+beef tallow
tissue: backfat
platform: HiScanSQ (Illumina)
gender: male
|
| Treatment protocol |
Immediately after slaughter, tissue samples were frozen in liquid nitrogen 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 HiScanSQ |
| |
|
| Description |
microRNA
|
| Data processing |
demultiplexing: bcl2fastq
quality control: FastQC
trimming off the 3' adapter sequences: UEA sRNA WorkbenchV4.6
filtering: UEA sRNA WorkbenchV4.6; parameters: 17-25 nt in length, minimum abundance of at least 6 supporting reads, tRNA and rRNA sequences excluded.
mapping: the filtered reads were mapped to Sscrofa10.2 genome and miRBase 22.1, using miRCat tool embeded in UEA sRNA WorkbenchV4.6. The following parameters were applied - default animal parameters, except for: minimum abundance (6), minimum length (17 nt) and maximum length (25 nt).
differential expression analysis: DESeq2 (a Bioconductor R-project package)
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: FASTA files after filtering and adaptor trimming, generated with the use of UEA sRNA Workbench V4.6. They include the number of reads of detected sequences.
|
| |
|
| Submission date |
Sep 15, 2021 |
| Last update date |
Sep 17, 2021 |
| 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 |
GPL21186 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN21441329 |
| SRA |
SRX12194760 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5579640_42s_AR_filter.fa.gz |
94.0 Kb |
(ftp)(http) |
FA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
