|
| Status |
Public on Apr 10, 2020 |
| Title |
PPRV control CD-21 pbmc subset_R1 |
| Sample type |
SRA |
| |
|
| Source name |
CD-21 cells at 0day post infection from infected group
|
| Organism |
Capra hircus |
| Characteristics |
cell type: CD-21 cells
infection status: control
|
| Treatment protocol |
Two groups including one control and one treated were used in the study. For both the group (control and infected) blood was collected from goats and pbmcs were isolated.The PBMCs subsets(T helper cells, T cytotoxic cells, B lymphocytes, and monocytes)were enriched by positive selection using indirect MACS technology.were collected and screened for the absence of PPRV antigen, and for the infected group tissues were isloated from goat infected with Izatnagar 94 PPRV at 9 day post infection. The tissues 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 subset of PBMCs of control and PPRV infected goats were isolated using the RNeasy Mini kit (Qiagen GmbH, Germany). The integrity and quantity of isolated RNA were assessed based on a Bioanalyzer (Agilent Technologies, Inc). The RNA integrity number (RIN) value of all the samples were found greater than 8, which is considered suitable for further processing. protocol. The integrity and quantity of isolated RNA were assessed based on a Bioanalyzer (Agilent Technologies, Inc). The RNA integrity number (RIN) value of all the samples was found greater than 8, which is considered suitable for further processing.
Library was prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NewEngland Biolabs Inc.) following the manufacturer’s protocol. Approximately, 100ng of RNA from each sample was used for RNA library preparation. The quality of the libraries was assessed on Bioanalyzer and further quantified using a Qubit 2.0 Fluorometer (Life technologies) and by qPCR. Libraries were sequenced on Illumina – NextSeq500 following manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Gene expression in CD-21 cells
|
| Data processing |
Initially, the quality-filtered reads from control and infected samples (0 days and 9 dpi) were mapped to Capra hircus genome using Bowtie2. The mapped reads were then assembled using RNA-Seq by expectation maximization (RSEM).
|
| |
|
| Submission date |
Jun 10, 2019 |
| Last update date |
Apr 10, 2020 |
| Contact name |
Ravi Kumar Gandham |
| E-mail(s) |
gandham71@gmail.com
|
| Phone |
+919458687850
|
| Organization name |
NIAB
|
| Street address |
Gowlidoddy
|
| City |
Hyderabad |
| State/province |
Telangana |
| ZIP/Postal code |
500032 |
| Country |
India |
| |
|
| Platform ID |
GPL21299 |
| Series (1) |
| GSE132429 |
Contrasting gene expression profiles of monocytes and lymphocytes from Peste-des-petits-ruminants virus infected goats |
|
| Relations |
| BioSample |
SAMN11998965 |
| SRA |
SRX6027732 |
