|
| Status |
Public on Mar 20, 2018 |
| Title |
VIR rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Cell line derived from an infected cow and used at low passage
|
| Organism |
Bos taurus |
| Characteristics |
theileria annulata infection status: infected
passage: 62
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of Theileria-infected leukocytes was isolated using the miRNA isolation kit (Thermo fisher scientific #AM1560) according to the manufacturer’s instructions. The quality and quantity of RNA was measured by Nanodrop spectrophotometer. Total RNA designated for miRNA experiments was extracted using the mirVana miRNA isolation kit (Thermo Fisher) using the manufacturer’s instructions. The quantity and quality checked by Qubit and Bioanalyzer 2100, respectively.
The miRNA libraries were prepared using the Truseq Small RNA Sample Preparation kit following the manufacturer’s instructions. Briefly, 1 μg of total RNA was adapter ligated at the 3’ and 5’ ends, reverse transcribed, barcoded then amplified with 11 PCR reactions. Then the cDNA was run on a 6% TBE PAGE gel (Novex, Life Technologies). After staining with SYBR Green the gel is visualized on a UV transluminator (Doc-It imaging system, UVP) and the cDNA constructs of a size between 145-160 bp were cut out and eluted from the gel, concentrated and the libraries validated, quantified and finally pooled.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
miRNA
processed data file: known_miRNA_ODE.count.txt
|
| Data processing |
bcl2fastq2 Conversion Software
Reads were trimmed and made non-redundant using Adaptor_trim.pl script from mirTools2 package
Trimmed reads were aligned on miRBAse v21 for Bos taurus genome and read counts performed using mirTools2 tool
differential miRNA analysis performed by DESeq2 tool
Genome_build: Bos taurus 4.6.1
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
Apr 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Arnab Pain |
| E-mail(s) |
arnab.pain@kaust.edu.sa
|
| Organization name |
King Abdullah University of Science and Technology
|
| Department |
Biological and Environmental Sciences and Engineering
|
| Street address |
Building 2, Level 4
|
| City |
Thuwal, Jeddah |
| ZIP/Postal code |
239556900 |
| Country |
Saudi Arabia |
| |
|
| Platform ID |
GPL23295 |
| Series (1) |
| GSE97706 |
miR-126-5p by direct targeting of JNK-interacting protein-2 (JIP-2) plays a key role in Theileria-infected macrophage virulence |
|
| Relations |
| BioSample |
SAMN06711915 |
| SRA |
SRX2734052 |
