|
| Status |
Public on Jul 15, 2021 |
| Title |
Rep6_S767 |
| Sample type |
SRA |
| |
|
| Source name |
SupT1
|
| Organism |
Human immunodeficiency virus 1 |
| Characteristics |
source: SupT1 human T cell line
strain: NL4-3
treatment: Post-selection
|
| Treatment protocol |
We infected SupT1 cells at low MOI (multiplicity of infection) with each library individually and measured the change in allele frequencies after approximately 6 generations of viral spread (Figure 3A)
|
| Growth protocol |
SupT1 human T-cell lines were maintained in RPMI (supplemented with 25 mM HEPES pH 7.4, 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin/streptomycin) at 37°C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from virions by ZR-96 Viral RNA extraction kits (Zymo) and eluted in 15 ul water. cDNA was amplified from 5uL of extracted RNA using the iScript Advanced (BioRad) cDNA synthesis.
PCR amplicons were made from DNA using primers specific to the Env LLP-2 region
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
HIV-1 RNA
Viral RNA harvested and sequenced after spread
|
| Data processing |
Library strategy: Amplicon-Sequencing
FASTQs were generated using bcl2fastq v2.17.1.14
Codons were counted using countDMS
Genome_build: HIV-1 NL4-3
Supplementary_files_format_and_content: tab
|
| |
|
| Submission date |
Jun 28, 2021 |
| Last update date |
Jul 17, 2021 |
| Contact name |
Jason Fernandes |
| E-mail(s) |
jason.d.fernandes@gmail.com
|
| Organization name |
UCSF
|
| Street address |
600 16th Street, Genentech Hall, Room S574, MC 2280
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL23868 |
| Series (1) |
| GSE179046 |
Functional and Structural Segregation of Overlapping Helices in HIV-1 |
|
| Relations |
| BioSample |
SAMN19918591 |
| SRA |
SRX11243584 |
