|
| Status |
Public on Jul 24, 2023 |
| Title |
PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 15, tech rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Macaca fascicularis |
| Characteristics |
tissue: Blood
cell type: PBMC
genotype: WT
animal id: 1407844
animal id supp: Survivor 1
Sex: female
outcome: survived
challenge: BDBV
time (days post infection): 15
treatment time: 30_min
treatment: VSV-BDBV-GP
tech rep: 1
|
| Growth protocol |
The BDBV used in this study, strain 200706291 (GenBank accession no. MK028856.1), was isolated from a fatal human case in western Uganda during the outbreak in 2007. The challenge stock of BDBV was propagated on Vero E6 cells twice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At least three million PBMC were inactivated with Trizol LS buffer (Thermo Fisher Scientific) for isolation of RNA. RNA was isolated using Direct-zol RNA Miniprep purification kits (Zymo Research) following the directions of the manufacturer with the optional DNAse I treatment and subsequent wash steps. RNA was eluted in 30ul of DNase/RNase-free water.
An Illumina Ribo-Zero Stranded kit was used to deplete ribosomal RNA (rRNA) and construct cDNA libraries according to the protocol provided by the manufacturer. RNA was fragmented, converted to double-stranded cDNA, and adapters ligated to each strand. The resulting base-pair cDNA fragments were then amplified by PCR. Each library was prepared with a unique indexed adapter for multiplexing. Multiplexed libraries were subjected to paired-end 75 base pair sequencing using the Illumina NextSeq550 PE platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Processed data file col_name: nhp1407844_05_417
|
| Data processing |
Sequencing quality of each sequenced sample was analyzed with fastQC (version 0.11.7).
Raw fastq files were trimmed with trimmomatic (version 0.36) with “LEADING” and “TRAILING” set to cut sequences below quality Phred score of 3 from the beginning or end of the read, respectively. Sequences below 15bp were automatically rejected.
STAR RNA-seq aligner (Dobin & Gingeras, 2015) version 2.5.3a was then used to create an index containing the cynomolgus macaque (Version 5.0), BDBV, and VSV genomes. Trimmed reads were aligned to these genomes using STAR.
The number of reads associated with each transcript was then counted with featureCounts (subread package version 1.6.2).
Genes with multiple possible transcripts were combined to get the number of reads per gene using DESeq2 (version 1.32.0). DESeq2 was used to normalize library sizes and measure differential expression between pre-infection and post infection samples.
Assembly: Macaca_fascicularis_5.0 (GCA_000364345.1)
Supplementary files format and content: bdbv_2019_30min_raw_counts.xlsx: total gene counts, pre-normalization by DESeg2
|
| |
|
| Submission date |
Jul 17, 2023 |
| Last update date |
Jul 24, 2023 |
| Contact name |
Thomas Geisbert |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Texas Medical Branch
|
| Department |
Microbiology and Immunology
|
| Lab |
Geisbert
|
| Street address |
301 University Blvd
|
| City |
Galveston |
| State/province |
TX |
| ZIP/Postal code |
77555 |
| Country |
USA |
| |
|
| Platform ID |
GPL27448 |
| Series (1) |
| GSE237547 |
A recombinant vesicular stomatitis virus-based vaccine provides postexposure protection against Bundibugyo ebolavirus infection |
|
| Relations |
| BioSample |
SAMN36504524 |
| SRA |
SRX21050487 |
