|
| Status |
Public on Feb 16, 2016 |
| Title |
MT4 Control 2 RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
MT4 T-cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: control
cell line: MT4
|
| Treatment protocol |
Treated cells were infected with HIV-1 LAI virus (106 cpm of RT activity/106 cells) for 12 hours, centrifuged, washed with PBS, and resuspended in RPMI/10% FBS
|
| Growth protocol |
HIV-1 LAI virus was produced by transfection of 293T cells with the proviral pLAI2 plasmid (NIH AIDS program) at 3 µg/106 cells using Lipofectamine 2000 (Invitrogen), according to the manufacturer’s instructions. After 4 h incubation, the medium was replaced with DMEM supplemented with 10% foetal bovine serum (FBS). Two days after transfection, the virus-containing supernatant was collected and filtered.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using TRIzol reagent (Invitrogen), poly(A) RNA purified using oligo dT Dynabeads (Invitrogen), and MeRIP-Seq performed using Cell 2012 protocol.
Illumina TruSeq mRNA Stranded LT
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
GL-Control-2.star.peaks.bed
|
| Data processing |
Aligner: STAR 2.3.0e
Peak calling: MeRIPPeR 0.9.1
Coverage: bedtools 2.24.0
Genome_build: hg19 + HIV-1
Supplementary_files_format_and_content: Peak files in bed file format generated with MeRIPPeR 0.9.1, coverage files computed using bedtools 2.24.0
|
| |
|
| Submission date |
Oct 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher E Mason |
| E-mail(s) |
chm2042@med.cornell.edu
|
| Organization name |
Weill Cornell Medical College
|
| Department |
Physiology and Biophysics
|
| Lab |
Christopher Mason Lab
|
| Street address |
1305 York Ave
|
| City |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE74016 |
Dynamics of the human and viral m6A RNA methylomes during HIV-1 infection of T cells |
|
| Relations |
| BioSample |
SAMN04166350 |
| SRA |
SRX1335345 |
