|
| Status |
Public on Nov 26, 2019 |
| Title |
14029_7v_LRL Kp9 _vaccinated_Day7 |
| Sample type |
SRA |
| |
|
| Source name |
Lung Right Lobe
|
| Organism |
Macaca fascicularis |
| Characteristics |
animal id: Kp9
vaccination: ST258 CPS2
tissue: Lung Right Lobe
treatment: vaccinated
time: Day7
|
| Treatment protocol |
Five sham-vaccinated animals received 0.6 ml of injection grade saline combined with adjuvant instead of purified CPS2;Five animals were inoculated with up to 500 μg of purified K. pneumoniae CPS2 in 0.6 ml injection grade saline mixed 1:1 with TiterMax Gold adjuvant (Sigma-Aldrich).
|
| Growth protocol |
CPS2 was extracted from bacterial culture supernatant, residual endotoxin was inactivated by incubation of purified CPS2 with 0.1 N NaOH in 95% ethanol for 1 h at 37C. The pH of the solution was neutralized with 2 N acetic acid and CPS2 was collected by centrifugation at 2000g for 10 min. The pellet was air dried and resuspended in sterile water
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified initially by using a PureLink RNA Mini Kit (Life Technologies, Carlsbad, CA). DNA was removed from purified RNA samples by treatment with TURBO DNase (Life Technologies, Grand Island, NY) for 45 min at 37 C, and RNA was purified again using an RNeasy Mini Kit (Qiagen
Truseq RNA-seq with Poly dT pullout
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
bcl2fastq.pl basecall converter v2.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Macaque whole genome using hisat2
normalization and comparisons were run using deseq2 on the original file host_matrix30.txt
Genome_build: GCF_000364345.1_Macaca_fascicularis_5.0_genomic.fna
Supplementary_files_format_and_content: filtered, aligned, raw counts from all samples in one matrix;
|
| |
|
| Submission date |
Sep 09, 2019 |
| Last update date |
Nov 26, 2019 |
| Contact name |
Dan Sturdevant |
| E-mail(s) |
[email protected]
|
| 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 |
GPL27448 |
| Series (1) |
| GSE137135 |
Vaccine protection against multidrug-resistant Klebsiella pneumoniae in a non-human primate model of severe lower respiratory tract infection |
|
| Relations |
| BioSample |
SAMN12717752 |
| SRA |
SRX6821363 |
