|
| Status |
Public on Feb 29, 2016 |
| Title |
H9 uninfected |
| Sample type |
SRA |
| |
|
| Source name |
T-cell RNA
|
| Organism |
Homo sapiens |
| Characteristics |
age: 1 week
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 uninfected H9 T-cell line
|
| 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 |
SAMN03854510 |
| SRA |
SRX1091889 |
