|
| Status |
Public on Sep 01, 2023 |
| Title |
1PAR |
| Sample type |
SRA |
| |
|
| Source name |
mammary parenchyma
|
| Organism |
Bos taurus |
| Characteristics |
tissue: mammary parenchyma
treatment: control
|
| 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 |
Total RNA was extracted using Direct-zol RNA Mini Prep kit (Zymo Research). 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).
The 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 until further use.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
DATA-DESeq2-results-with-normalized.csv
|
| Data processing |
demultiplexing: bcl2fastq
quality control: FastQC
trimming off the 3' adapter sequence and length filtering (≤18nt discarded): TrimGalore
miRNA annotation and prediction: sRNAtoolbox-sRNAbench (number of allowed mismatches: 1, minimum read count: 6) with reference to miRBase 22.1
read count extraction, normalization and differential expression analysis: DESeq2 (a Bioconductor R-project package)
Assembly: ARS-UCD1_2_
Supplementary files format and content: CSV file with normalized abundance measurements
|
| |
|
| Submission date |
May 01, 2023 |
| Last update date |
Sep 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 |
GPL23055 |
| Series (1) |
| GSE231434 |
MicroRNA profiling of mammary gland and liver tissue of cows under different feeding conditions (control, restricted amount of milk replacer, milk replacer ad libitum) |
|
| Relations |
| BioSample |
SAMN34505913 |
| SRA |
SRX20176780 |
