|
| Status |
Public on May 28, 2020 |
| Title |
Day3_2 |
| Sample type |
SRA |
| |
|
| Source name |
Day3_CD3-, 28.4+ IEL-NK cells isolated from duodenum
|
| Organism |
Gallus gallus |
| Characteristics |
sample group: chicken infected by vvIBDV for 3 days
virus strain: vvIBDV_UPM0081
tissue: Duodenum
cell type: CD3-, 28.4+ IEL-NK cells
|
| Treatment protocol |
infected by vvIBDV (UPM0081) at a dosage of 103 EID50/0.1ml
|
| Growth protocol |
specific-pathogen-free (SPF) embryonated chicken eggs were obtained from Veterinary Research Institute, Ipoh, Perak and hatched in our laboratory under sterile conditions. The chicken was transferred to the Biosafety level-2 facility at our animal house where they were fed with pelleted feed and supplied with water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from enriched IEL-NK cells using the trizol reagent. The mRNA was captured from total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module kit
The mRNA sample was proceeded to the library prep using the ScriptSeq V2 RNA-Seq library prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Chicken_UPM_D3_2
|
| Data processing |
Fastq files were generated from BCL files using the bcl2fastq software
the fastq files were loaded inside the CLC Genomics Workbench for quality and adapter trimming
the filtered fastq files were proceeded for alignment to chicken genome using CLC Genomics Workbench
The differential expression analysis was conducted to find out the DE genes
Genome_build: Galgal4_ensembl
Supplementary_files_format_and_content: Read counts and expression value
|
| |
|
| Submission date |
Dec 17, 2018 |
| Last update date |
May 28, 2020 |
| Contact name |
Boo Sook Yee |
| E-mail(s) |
rinoa1685@gmail.com
|
| Phone |
+60128319568
|
| Organization name |
Universiti Putra Malaysia
|
| Department |
Institute of Bioscience
|
| Lab |
Laboratory of Vaccine & Immunotherapeutics
|
| Street address |
Universiti Putra Malaysia
|
| City |
Serdang |
| State/province |
Selangor |
| ZIP/Postal code |
43400 |
| Country |
Malaysia |
| |
|
| Platform ID |
GPL19005 |
| Series (1) |
| GSE123920 |
Gene Expression Study of Innate Immune Response of Chicken Intraepithelial lymphocyte natural killer cells to very virulent Infectious Bursal Disease Virus (vvIBDV) |
|
| Relations |
| BioSample |
SAMN10601916 |
| SRA |
SRX5139521 |
