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| Status |
Public on Jan 03, 2023 |
| Title |
Deciphering the resiquimod induced toll-like receptor signalling pathway in chickens |
| Organism |
Gallus gallus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Resiquimod (R-848) is a synthetic TLR7 agonist. This study was targeted to understand the signaling molecules involved in the Resiquimod (R-848) mediated TLR7 stimulation in the chicken and specifically for Th1 and Th2 type of immune responses. For this, transcriptome data (RNA-seq) was generated from RNA extracted at 24 hour from spleen tissues (1 each) of both control (untreated) and chicken administered with R-848 (intra muscular route). Upregulated and downregulated genes were identified following using transcriptome analysis pipeline Geo2RNAseq_0.99.9 (https://anaconda.org/xentrics/r-geo2rnaseq). Within the pipeline, the reads were quality checked using FastQC, quality trimming performed with Trimmomatic (Bolger et al., 2014) and reference genome (Gallus gallus: GRCg6a (GCA_000002315.5)) mapping was carried out using TopHat2 (Kim et al., 2013). Differently expressed genes (DEGs) were identified using baySeq (Hardcastle and Kelly, 2010). Functional annotation of DEGs were carried out using g:Profiler (Reimandet al., 2016; http://biit.cs.ut.ee/gprofiler/). Among the 5884 DEG, eight genes enriched in biological processes associated to signal transduction (MAPK14, MAP3K8, PIK3CD, STAT1, STAT3, MAPK11 LRRK2, and GATA3) were considered for further validation. Among the eight significant DEGs, MAPK14, MAP3K8, PIK3CD, STAT1 and STAT3 were up-regulated while MAPK11, LRRK2 and GATA3 transcripts were down-regulated in the R-848 treated birds evidenced by transcriptomic data.
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| Overall design |
Chicken spleen RNA profiles of treatment (post 24 hour R-848 administed) and control were generated by deep sequencing using Illumina sequencing technology
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| Contributor(s) |
Kappala D, Thomas P, Saravanan R |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jul 20, 2021 |
| Last update date |
Jan 25, 2023 |
| Contact name |
SARAVANAN RAMAKRISHNAN |
| E-mail(s) |
dearsaromib@gmail.com
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| Organization name |
ICAR-Indian Veterinary Research Institute
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| Street address |
Izatnagar
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| City |
Bareilly |
| State/province |
Uttar Pradesh |
| ZIP/Postal code |
243122 |
| Country |
India |
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| Platforms (1) |
| GPL19787 |
Illumina NextSeq 500 (Gallus gallus) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA748253 |
| SRA |
SRP329077 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE180434_DEG_stats.csv.gz |
1.7 Mb |
(ftp)(http) |
CSV |
| GSE180434_gene_counts.csv.gz |
156.5 Kb |
(ftp)(http) |
CSV |
| GSE180434_gprofiler_results.txt.gz |
158.2 Kb |
(ftp)(http) |
TXT |
| GSE180434_rpkm_val.csv.gz |
402.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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