|
| Status |
Public on Nov 01, 2023 |
| Title |
SupT1, Active-infected, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
SupT1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SupT1
cell type: T lymphoblast
genotype: WT
treatment: HIV GKO infection
time: 4 days post infection
|
| Treatment protocol |
SupT1 cells were infected with HIVGKO virus at an multiplicity of infection of 0.1 by spinoculation (3000rpm, 30min, 30C). Virus-infected or uninfected cells were cultured for 4 days in a 37C incubator with 6% CO2. Uninfected or HIV-1 active-infected (mKO2+GFP+) and latent- infected (mKO2+GFP-) SupT1 cells were flow sorted using a Biorad S3 cell sorter
|
| Growth protocol |
SupT1 cells were cultured in RPMI media supplemented with 10% fetal bovine serum (FBS) and 1% each of penicillin, streptomycin and glutamine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from flow-sorted cells using TRIzol reagent (Invitrogen) according to manufacturer’s protocol, followed by treatment with DNase (Turbo DNAse-free kit, Invitrogen)Ribosomal RNA (rRNA) was removed from the total RNA (50ng) using NEBNext rRNA Depletion kit v2 (Human/Mouse/Rat, New England Biolab), according to manufacturer’s instructions.
The rRNA-depleted samples were used for stranded library preparation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw RNA-seq reads were first analyzed with FastQC for quality control and the processed through Trim Galore for removal of low quality reads and the Illumina sequencing adapters
The trimmed, high-quality reads were aligned to the Ensembl human reference genome (GRCh38 v86) using the STAR aligner software
Raw reads count for each gene were obtained using -quantmode of GeneCounts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts
|
| |
|
| Submission date |
Aug 31, 2022 |
| Last update date |
Nov 01, 2023 |
| Contact name |
Gabrielle Lê-Bury |
| E-mail(s) |
gl489@cornell.edu
|
| Organization name |
Cornell University
|
| Street address |
930 campus road
|
| City |
Ithaca |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE212463 |
HIV-1 latent infection triggers broader transcriptional changes in protein-coding and long non-coding RNAs than active infection of SupT1 cells (RNA-Seq) |
| GSE212464 |
HIV-1 latent infection triggers broader transcriptional changes in protein-coding and long non-coding RNAs than active infection of SupT1 cells |
|
| Relations |
| BioSample |
SAMN30619178 |
| SRA |
SRX17386430 |
