|
| Status |
Public on Oct 22, 2021 |
| Title |
K_6 [20189_S12] |
| Sample type |
SRA |
| |
|
| Source name |
Macaca nemestrina infected with Kyasanur forest disease virus at day 6
|
| Organism |
Macaca nemestrina |
| Characteristics |
agent: Kyasanur forest disease virus
time point: day 6
|
| Treatment protocol |
Virus inoculations were performed with the indicated virus diluted in sterile PBS. For subcutaneous (sc) infections, 1x105 pfu was delivered in a single injection between the shoulder blades (1 ml volume)
|
| Growth protocol |
Twelve female PTMs aged 10 to 16 years of age were housed in a humidity, temperature, and light controlled facility in adjacent cages for social interaction. Virus seed stocks were propagated once on Vero cells, and virus working stocks were aliquoted and frozen in liquid nitrogen tanks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 140 ml plasma using the QIAamp Viral RNA Mini Kit (Qiagen). RNA was irradiated (10 megarad) for removal from the BSL4 according to established sample removal protocols (54). Following removal, cDNA was generated using SuperScript VILO cDNA Synthesis Kit (ThermoFisher).
100 ng of RNA was used for initial treatment with the Qiagen FastSelect -H/M/R and -Globin kit to inhibit cDNA synthesis of rRNA and globin transcripts. The two viral stocks were not rRNA/Globin treated. The only modification was to reduce the initial fragmentation step to 2 minutes to account for the degradation of the RNA. After incubation with the probes from the FastSelect kit, the samples proceeded with cDNA synthesis and library preparation following the Illumina Stranded RNA Prep, Ligation kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Raw fastq reads were trimmed of Illumina adapter sequences using cutadapt version 1.12
then trimmed and filtered for quality using the FASTX-Toolkit (Hannon Lab)
Remaining reads were aligned to the Mesocricetus auratus genome assembly version 1.0 using Hisat2 (Kim et al., 2015)
Reads mapping to genes were counted using htseq-count (Anders et al., 2015)
Differential expression analysis was performed using the Bioconductor package DESeq2 (Love et al., 2014)
Genome_build: NC_041754.1 Macaca mulatta : JF416958.1 Kyasanur forest disease virus strain P9605 : JF416954.1 Alkhumra hemorrhagic fever virus strain 200300001
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample and matrix table with normalized gene counts.
|
| |
|
| Submission date |
Oct 13, 2021 |
| Last update date |
Oct 22, 2021 |
| Contact name |
Dan Sturdevant |
| E-mail(s) |
dsturdevant@niaid.nih.gov
|
| Phone |
4063639248
|
| Organization name |
NIH
|
| Department |
NIAID
|
| Lab |
RTS
|
| Street address |
903 S 4th street
|
| City |
Hamilton |
| State/province |
MT |
| ZIP/Postal code |
59840 |
| Country |
USA |
| |
|
| Platform ID |
GPL30848 |
| Series (1) |
| GSE185797 |
A pigtailed macaque model for Kyasanur Forest disease virus and Alkhurma hemorrhagic disease virus pathogenesis |
|
| Relations |
| BioSample |
SAMN22242680 |
| SRA |
SRX12590492 |
