|
| Status |
Public on Aug 29, 2024 |
| Title |
Bird_610_MG-protein_Day0 |
| Sample type |
SRA |
| |
|
| Source name |
Whole blood
|
| Organism |
Serinus canaria |
| Characteristics |
tissue: Whole blood
subject: Bird_610
time: Day 0
disease: Unexposed
treatment: High protein diet
|
| Treatment protocol |
RNAlater was added to blood samples immediately upon collection. Samples were stored at 20°C for 24 hr then at -80°C until extraction. Canary RNA was extracted from whole blood on days 0, 14, and 21 post infection
|
| Growth protocol |
Canaries were housed individually in cages and provided with either a high protein (n = 20) or high lipid (n = 22) diet for 17 days prior to inoculation and throughout the experiment. On day 0, birds were inoculated in the palpebral conjunctiva of both eyes with either 0.025 mL of MG suspended in Frey’s media or with a sham of Frey’s media alone.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Zymo Direct-zol RNA Miniprep with TRI Reagent phase separation
NEXTflex™ Rapid Directional RNA-Seq Kit 2.0
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ES88_610_MG-protein_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv
|
| Data processing |
nf-core rnaseq version 3.10.1 pipeline was utilized with Nextflow version 22.10.3 [parameters: -profile singularity --featurecounts_group_type transcript_biotype --skip_markduplicates --aligner star_rsem --pseudo_aligner salmon]
Adapter trimming performed with TrimGalore! v 0.6.7 [parameters: nf-core default]
Mapping to genome performed with STAR v 2.7.10a [parameters: nf-core default]
Counts estimated from genes with RSEM v 1.3.1 [parameters: --strandedness reverse]
Differential expression was performed in EdgeR using expected counts and the quasi-liklihood (QL) framework with Benjamini-Hochberg FDR correction. Genes with less than 0.5 count per million (CPM) in more than 12 samples were excluded from the analysis.
Assembly: serCan2020
Supplementary files format and content: All files are tab delimited text files. One file is the STAR-RSEM gene count output (serinus_canaria_rsem.merged.gene_counts.tsv) and the other is the STAR-RSEM gene tpm values (serinus_canaria_rsem.merged.gene_tpm.tsv)
|
| |
|
| Submission date |
Jul 31, 2024 |
| Last update date |
Aug 29, 2024 |
| Contact name |
Carson Len Stacy |
| E-mail(s) |
clstacy.stat@gmail.com
|
| Organization name |
University of Arkansas
|
| Department |
Biological Sciences
|
| Lab |
Lewis
|
| Street address |
2692 Powell St
|
| City |
Springdale |
| State/province |
AR |
| ZIP/Postal code |
72764 |
| Country |
USA |
| |
|
| Platform ID |
GPL32262 |
| Series (1) |
| GSE273665 |
Diet driven differences in host tolerance are linked to shifts in global gene expression in a common avian host-pathogen system |
|
| Relations |
| BioSample |
SAMN42953989 |
| SRA |
SRX25532019 |
