|
| Status |
Public on Jan 03, 2023 |
| Title |
Chicken_control |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: Spleen
treatment: control
|
| Treatment protocol |
Resiquimod (R-848) was adminstered to a chicken (treatment ) and untreated bird was kept as control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At 24 hour post administration (p.i.), all chicken were euthanized humanely, spleen was harvested aseptically. Total RNA was extracted from spleen samples (1 each for treatment and control) usingTRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Quality Check (fastqc 0.11)
Quality trim (trimmomatic 0.36)
Mapping (tophat 2.1.0)
DEG Analysis (DESeq_1.28.0, DESeq2_1.16.1 and baySeq_2.10.0)
Functional annotation ( g:Profiler)
Genome_build: GRCg6a (GCA_000002315.5)
Supplementary_files_format_and_content: Three excel files representing gene counts (gene_counts), rpkm values (rpkm_val) and gene expression (DEG_stats) and one text file (gprofiler_results) representing functional annotation
|
| |
|
| Submission date |
Jul 20, 2021 |
| Last update date |
Jan 03, 2023 |
| Contact name |
SARAVANAN RAMAKRISHNAN |
| E-mail(s) |
dearsaromib@gmail.com
|
| Organization name |
ICAR-Indian Veterinary Research Institute
|
| Street address |
Izatnagar
|
| City |
Bareilly |
| State/province |
Uttar Pradesh |
| ZIP/Postal code |
243122 |
| Country |
India |
| |
|
| Platform ID |
GPL19787 |
| Series (1) |
| GSE180434 |
Deciphering the resiquimod induced toll-like receptor signalling pathway in chickens |
|
| Relations |
| BioSample |
SAMN20322075 |
| SRA |
SRX11503725 |
