|
| Status |
Public on Nov 01, 2023 |
| Title |
SupT1, Uninfected, ATAC, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
SupT1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SupT1
cell type: T lymphoblast
genotype: WT
treatment: HIV GKO infection
treatment: 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 |
genomic DNA |
| Extraction protocol |
100,000 cells were used to for transposition reaction (Illumina Tagment DNA TDE1 Enzyme and Buffer Kit). Tagmented DNA was purified with MinElute purification kit (Qiagen)
Tagmented DNA used for subsequent library preparation by PCR amplification using unique dual-indexing (Illumina Nextera i5 common adapter and i7 index adapter) primers. ATAC-seq libraries were purified using AMPure SPRI beads (Beckman Coulter)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Raw ATAC-seq reads were first processed by FastQC for quality control and then Illumina sequencing adapters were trimmed from paired-end reads using Cutadapt
The trimmed reads were aligned to human reference genome GRCh38 using BWA-MEM and the resulting alignment output were analyzed by SAMStat for quality control and then sorted by SAMtools
Post-alignment filtering was performed by SAMtools, ‘MarkDuplicates’ program of Picard tools as well as ENCODE ATAC-seq script assign_multimappers.py to remove PCR duplicates, secondary alignments and unmapped reads. Quality control of fragment size distribution was carried out by ATACseqQC
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include merged IDR peak 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 |
GPL30173 |
| Series (2) |
| GSE212462 |
HIV-1 latent infection triggers broader epigenomic changes in protein-coding and long non-coding RNAs than active infection of SupT1 cells (ATAC-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 |
SAMN30619175 |
| SRA |
SRX17386400 |
