|
| Status |
Public on May 10, 2018 |
| Title |
PBMCs_indigenous_21dpv |
| Sample type |
SRA |
| |
|
| Source name |
PBMCs collected at 21 days post CSF vaccination from indigenous pigs
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Indigenous
infection status: 21 days post CSF vaccination
|
| Treatment protocol |
Three indigenous and crossbred pigs were vaccinated and PBMCs were collected at 7 and 21 days post vaccination. Also MDMs of indigenous and crossbred pigs were harvested 60 hours post infection with CSF virulant virus. The crossbred were taken as control and the gene expression were compared in indigenous pigs. The isolated PBMCs of both groups were collected in RNase free 1.5 ml centrifuge tube in RNA later.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each of the collected samples was isolated using the RNeasy Mini kit (Qiagen GmbH, Germany) according to the manufacturer’s protocol. The integrity and quantity of isolated RNA were assessed on a Bioanalyzer (Agilent Technologies, Inc). The RNA integrity number (RIN) value of all the samples was found greater than 7, which is considered suitable for further processing.
Library was prepared using mRNA Library Prep Kit following the manufacturer’s protocol. The quality of the libraries was assessed on Bioanalyzer and quantification was done using a Qubit 2.0 Fluorometer (Life Technologies) and by quantitative real-time PCR. Libraries wee sequenced on Illumina – HiSeq2000 following manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
mRNA expression in PBMCs of indigenous pigs at 21 days post CSF vaccination
|
| Data processing |
The fastq files containing mRNA sequencing reads, the adapters were trimmed from the reads. The low quality reads (phred score < 25 and read length <50) were trimmed using (PRINSEQLITET). Hereafter, known mRNAs were identified by annotating the clean reads to reference genome of pig. The counts obtained were analyzed using DESeq2, edgeR and EBSeq for identifying differentially expressed mRNAs under CSF infection. The common differentially expressed genes were further selected for downstrem analysis.
Supplementary_files_format_and_content: tab-delimited text files include mRNA gene name, expression values (log2 fold change) and significant p-value using edgeR softwares
|
| |
|
| Submission date |
May 09, 2018 |
| Last update date |
Jun 13, 2018 |
| Contact name |
AMIT KUMAR |
| Organization name |
Indian Veterinary Research Institute
|
| Department |
Animal Genetics
|
| Lab |
Computational Genomics
|
| Street address |
Izatnagar
|
| City |
Bareilly |
| State/province |
Uttar Pradesh |
| ZIP/Postal code |
243122 |
| Country |
India |
| |
|
| Platform ID |
GPL20983 |
| Series (1) |
| GSE114229 |
Expression profile of mRNAs in PBMCs infected with CSF vaccine virus and Monocyte derived macrophages infected with virulent CSF virus of crossbred and indigenous pigs |
|
| Relations |
| BioSample |
SAMN09098491 |
| SRA |
SRX4059034 |
