|
| Status |
Public on Apr 20, 2023 |
| Title |
EF19-5-9 |
| Sample type |
SRA |
| |
|
| Source name |
skin
|
| Organism |
Cavia porcellus |
| Characteristics |
tissue: skin
immunization: ticks 2 bites
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation (Qiagen Rneasy)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
bite
4 days post tick bite
|
| Data processing |
reads were trimmed for quality and filtered for length using trimmomatic. Only those bases with quality values of Q30+ and read lengths of 45+ were used for further analysis. The trimmed reads were aligned to guinea pig genome (Cavea porcellus, Cavpor 3.0 from Ensembl)
The alignment files were processed with stringTie, and ballgown to generate per gene counts. These count matrices were processed further with R and DESeq to obtain significantly differentially expressed genes
Genome_build: Cavpor 3.0 from Ensembl
Supplementary_files_format_and_content: TSV files with TPM values in each cell. All genes on rows, all samples in columns.
|
| |
|
| Submission date |
Apr 20, 2020 |
| Last update date |
Apr 20, 2023 |
| Contact name |
Erol Fikrig |
| E-mail(s) |
erol.fikrig@yale.edu
|
| Organization name |
Yale University School of Medicine
|
| Street address |
300 Cedar Street
|
| City |
New Haven |
| ZIP/Postal code |
06437 |
| Country |
USA |
| |
|
| Platform ID |
GPL28437 |
| Series (2) |
| GSE148967 |
Repeat tick exposure elicits distinct immune responses in guinea pigs and mice [guinea pig] |
| GSE148969 |
Repeat tick exposure elicits distinct immune responses in guinea pigs and mice |
|
| Relations |
| BioSample |
SAMN14646271 |
| SRA |
SRX8143597 |
