|
| Status |
Public on Nov 27, 2023 |
| Title |
P8_S12 |
| Sample type |
SRA |
| |
|
| Source name |
Mononuclear cells from the plasma of HIV1-infected humanized mouse, 353M2
|
| Organism |
Human immunodeficiency virus 1 |
| Characteristics |
model: HIV1-infected humanized mouse
mouse_id: 353M2
|
| Growth protocol |
Three different HIV-1, CH185 wild-type, the CH185 deltaP1 mutant, and the CH185 deltaP2 mutant were co-inoculated into nine humanized mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
for plasma samples, QIAamp viral RNA mini kit (Qiagen); for speen samples, QIAamp RNA blood mini kit (Qiagen)
DNA library preparation kit (NEB)
OTHER: RT-PCR amplicon sequencing
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Read trimming and filtering were performed with Trimmomatic (version 0.39).
Fastq file was converted to fasta file.
Reads were mapped to the sequence of three genotypes of HIV-1 (CH185 wild-type, the CH185_dPTAP1 mutant, and the CH185_dPTAP2) using BLASTn (version 2.6.0).
Reads were assigned to the top hit genotype. If tie, the read was discarded.
Reads assigned to each genotype were counted.
Genome_build: CH185_WT; AGGGAAAATCTGGCCTTCCAACaaggggaggccagggaatttccttCAGAACAGAGCAGAGCCAACAGCCCCACCAGCAGAGAGCTTCCCTCAGAGCAGACCAGAGCCAACAGCTCCACCAGCAGAGAGCTTCGCTCCGAAGCAGGAGCCGAGAGAGAGGGAACCTTTAATTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAATAAaagtagggggccaggtaaaggaggctctcttagacacaggagcagatgatacagtattagaagaaataaatttGCCAGGAAAATGGAAACC
Genome_build: CH185_dPTAP1; AGGGAAAATCTGGCCTTCCAACAAGGGGAGGCCAGGGAATTTCCCTCAGAGCAGACCAGAGCCAACAGCTCCACCAGCAGAGAGCTTCGCTCCGAAGCAGGAGCCGAGAGAGAGGGAACCTTTAATTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAATAAaagtagggggccaggtaaaggaggctctcttagacacaggagcagatgatacagtattagaagaaataaatttGCCAGGAAAATGGAAACC
Genome_build: CH185_dPTAP2; AGGGAAAATCTGGCCTTCCAACAAGGGGAGGCCAGGGAATTTCCTTCAGAACAGAGCAGAGCCAACAGCCCCACCAGCAGAGAGCTTCGCTCCGAAGCAGGAGCCGAGAGAGAGGGAACCTTTAATTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAATAAaagtagggggccaggtaaaggaggctctcttagacacaggagcagatgatacagtattagaagaaataaatttGCCAGGAAAATGGAAACC
Supplementary_files_format_and_content: blast output
|
| |
|
| Submission date |
Dec 01, 2020 |
| Last update date |
Nov 27, 2023 |
| Contact name |
Kei Sato |
| E-mail(s) |
su9ark@gmail.com
|
| Phone |
81364092212
|
| Organization name |
The Institute of Medical Science, The University of Tokyo
|
| Department |
Department of Microbiology and Immunology
|
| Lab |
Division of Systems Virology
|
| Street address |
4-6-1 Shiroganedai
|
| City |
Minato-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
1088639 |
| Country |
Japan |
| |
|
| Platform ID |
GPL23868 |
| Series (1) |
| GSE162442 |
Viral RNA-sequencing for the detection of the viruses replicating in humanized mice |
|
| Relations |
| BioSample |
SAMN16969985 |
| SRA |
SRX9614696 |
