|
| Status |
Public on Mar 04, 2021 |
| Title |
12_low proviral copies |
| Sample type |
SRA |
| |
|
| Source name |
whole blood
|
| Organism |
Capra hircus |
| Characteristics |
tissue: blood
viral load: low
breed: Carpathian goat
gender: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was isolated from whole blood of goats selected based on of provirus copy number, and which were the most homogeneous within the groups. Isolation was performed using MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit (Thermo Fisher Scientific), according to the protocol. The possible RNA contamination with DNA was removed using TURBO DNase™ (Thermo Fisher Scientific). The quality and quantity of obtained RNA were check using Nanodrop 2000 Spectrophotometer (Thermo Scientific) and TapeStation 2200 System (Agilent) using Agilent RNA ScreenTape (Agilent). The samples with RIN (RNA integrity number) value above 8 were used to further analysis.
The cDNA libraries were prepared from 300ng of total RNA by using TruSeq RNA Kit v2 kit (Cat#FC-122-1001) according to protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
12
|
| Data processing |
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters, reads of low quality (<20 phred quality) and shorter than 35.
The raw reads were aligned to the Capra hircus ARS1 (GCA_001704415.1) with Tophat software on default settings
The obtained reads were counted with the use of htseq-count which were the input for DESeq2 analysis
The differential expression estimation was proceed with utilization of DESeq2 Bioconductor R-project package.
Genome_build: Capra hircus ARS1 (GCA_001704415.1)
Supplementary_files_format_and_content: Text files (.txt) containing raw gene counts used for DESeq2 analysis
|
| |
|
| Submission date |
Mar 03, 2021 |
| Last update date |
Mar 04, 2021 |
| Contact name |
Tomasz Szmatola |
| E-mail(s) |
tomasz.szmatola@gmail.com
|
| Organization name |
University of Agriculture in Krakow
|
| Department |
OMEI
|
| Street address |
Redzina 1c
|
| City |
Kraków |
| ZIP/Postal code |
30-248 |
| Country |
Poland |
| |
|
| Platform ID |
GPL19149 |
| Series (1) |
| GSE168160 |
Transcriptome-wide search for Carpathian goat factors associated with proviral load of small ruminant lentiviruses in goats |
|
| Relations |
| BioSample |
SAMN18128066 |
| SRA |
SRX10228832 |
