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| Status |
Public on Feb 19, 2021 |
| Title |
CD335 subset of Goat at day 0 |
| Sample type |
SRA |
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| Source name |
PBMCs of Goat at day 0
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| Organism |
Capra hircus |
| Characteristics |
cell type: CD335
infection status: 0 day
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| Treatment protocol |
Goat and Sheep were subjected to Sungri/96 PPRV vaccination and PBMCs were isolated from them at 0 day (control i.e. just before vaccination) and before the development of antibody response (5 days post vaccination i.e. 5dpv). The RNA was isolated from each subsets of PBMCs of both species.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each subset-CD4+, CD8+, CD14+, CD21+ and CD335+ of PBMCs of control (Goat & Sheep) and vaccinated (Goat & Sheep) 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.
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). Libraries were sequenced on Illumina – NextSeq500 following manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Gene expression in CD335
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| Data processing |
Initially, the quality-filtered reads from control and infected samples (0 days and 5 days post vaccination) were mapped to Goat/Sheep genome using Bowtie2. The mapped reads were then assembled using RNA-Seq by expectation maximization (RSEM).
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| Submission date |
Jul 31, 2020 |
| Last update date |
Feb 19, 2021 |
| Contact name |
Ravi Kumar Gandham |
| E-mail(s) |
gandham71@gmail.com
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| Phone |
+919458687850
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| Organization name |
NIAB
|
| Street address |
Gowlidoddy
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| City |
Hyderabad |
| State/province |
Telangana |
| ZIP/Postal code |
500032 |
| Country |
India |
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| Platform ID |
GPL21299 |
| Series (1) |
| GSE155504 |
Transcriptional profiling of different subsets of PBMCs-CD4+, CD8+, CD14+, CD21+, CD335+ reveals differential response to Sungri/96 PPRV vaccination in Goat and Sheep |
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| Relations |
| BioSample |
SAMN15689710 |
| SRA |
SRX8861347 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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