|
| Status |
Public on Dec 18, 2023 |
| Title |
Alpha unvaccinated replicate5 |
| Sample type |
SRA |
| |
|
| Source name |
right lung caudal lobe
|
| Organism |
Mesocricetus auratus |
| Characteristics |
tissue: right lung caudal lobe
vaccination: PBS control
viral challenge: Alpha
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Right lung caudal lobe was harvested from the animals and homogenized in trizol. RNA purification was performed with the kit RiboPure™ RNA Purification Kit following manufacturer’s instructions.
Sequencing libraries were generated with the Illumina Total RNA Prep with Ribo-Zero Plus kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing adapters were trimmed from reads using Cutadapt.
Trimmed reads were pseudoaligned to the golden hamster transcriptome with Kallisto.
Estimated gene counts were obtained by combining transcript-level counts using tximport.
Assembly: MesAur1.0
Supplementary files format and content: count_matrix.txt: tab-separated estimated read counts per gene
Supplementary files format and content: tpm_matrix.txt: tab-separated transcripts per million (TPM) per gene
|
| |
|
| Submission date |
Nov 02, 2023 |
| Last update date |
Dec 18, 2023 |
| Contact name |
Max Chang |
| E-mail(s) |
mchang@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL28997 |
| Series (1) |
| GSE246866 |
Breakthrough infections by SARS-CoV-2 variants boost cross-reactive hybrid immune responses in mRNA-vaccinated Golden Syrian Hamsters |
|
| Relations |
| BioSample |
SAMN38081971 |
| SRA |
SRX22341787 |
