|
Status |
Public on Feb 29, 2016 |
Title |
H9 infected |
Sample type |
SRA |
|
|
Source name |
T-cell RNA
|
Organism |
Homo sapiens |
Characteristics |
age: 1 week post-infection cell line: H9
|
Treatment protocol |
H9 T-cells were infected with clonal HIV-1 obtained by transfecting the 293T cells with pNL43.
|
Growth protocol |
H9 T-cells were growing in RPMI+FBS medium
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Qiagen's RNEasy mini kit was used to extract cellular RNA from infected and uninfected T cells. RNA libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
RNA from H9 T-cell line infected with NL4-3 strain of HIV-1
|
Data processing |
Quality control analysis: trimming adaptors using Trimmomatic, and pruning reads using Fastx toolkit Cleaned up reads were aligned to reference human transcriptome using Tophat2 Tophat2 output was supplied to Cuffdiff for identifying gene-expression for all the genes in two samples. Genome_build: Homo_sapiens.GRCh37.75.gtf Supplementary_files_format_and_content: Tab delimited file that is given by Cuffdiff. Each row has a gene, its expression in infected and uninfected Tcells, and the log2(fold change in gene expression), among other information such as chromosomal location of the gene.
|
|
|
Submission date |
Jul 10, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Aditi Gupta |
E-mail(s) |
aditi9783@gmail.com
|
Organization name |
Rutgers University
|
Department |
Medicine
|
Street address |
185 South Orange Ave, MSB-A920G
|
City |
Newark |
State/province |
NEW JERSEY |
ZIP/Postal code |
07103 |
Country |
USA |
|
|
Platform ID |
GPL16791 |
Series (1) |
GSE70785 |
Differentially Expressed Pseudogenes in HIV-1 Infection |
|
Relations |
BioSample |
SAMN03854508 |
SRA |
SRX1091888 |