|
| Status |
Public on Nov 02, 2019 |
| Title |
PBMCs of Tharparkar cattle under heat stress at day 7, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
PBMCs of Tharparkar cattle under heat stress at day 7
|
| Organism |
Bos taurus |
| Characteristics |
breed: Tharparkar
stress: heat stress
time: 7 days
cell type: PBMC
|
| Treatment protocol |
Tharparkar and Crossbred were subjected to heat for a period of 7 day and PBMCs were isolated from them. RNA was isolated from PBMCs of both genetic groups before ( 0 days ) and post heat stress (7 day ) .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each subset of PBMCs of control and heat stressed cattle 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.
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 PBMCs
|
| Data processing |
Initially, the quality-filtered reads from control and infected samples (0 days and 7 days post treatment) were mapped to bovine genome using Bowtie2. The mapped reads were then assembled using RNA-Seq by expectation maximization (RSEM).
Supplementary_files_format_and_content: TPMs, FPKMs
|
| |
|
| Submission date |
Aug 29, 2019 |
| Last update date |
Nov 02, 2019 |
| 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 |
GPL23055 |
| Series (1) |
| GSE136652 |
Transcriptional profiling reveals differential response to heat stress in Tharparker and Crossbred Cattle |
|
| Relations |
| BioSample |
SAMN12659550 |
| SRA |
SRX6778415 |
