|
| Status |
Public on Nov 01, 2014 |
| Title |
Ad8_DC_D1 |
| Sample type |
RNA |
| |
|
| Source name |
CD4+ Tcell
|
| Organism |
Homo sapiens |
| Characteristics |
donor: D1
treatment: DC
coculture: NL(AD8)-nef/EGFP (MOI 5)
sorted population: SNARFhiEGFP- CD4+ Tcell
|
| Treatment protocol |
Sorted SNARFhiEGFP- CD4+ T cells were lysed in RLT buffer and stored at -80oC prior to RNA extraction
|
| Growth protocol |
SNARF labelled resting CD4+ T cells were cultured with or without syngeneic DC in the presence or absence of NL(AD8)-nef/EGFP (MOI 5) for 5 days, at which time SNARFhiEGFP- CD4+ T cells were sorted for gene expression analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
totalRNA using Qiagen RNeasy Micro Kit by the Laboratory of Dr. Sekaly at University of Montreal
|
| Label |
Biotin
|
| Label protocol |
The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.
|
| |
|
| Hybridization protocol |
Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-8 V3 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at CGC.
|
| Scan protocol |
The arrays were scanned using an Illumina BeadArray scanner and quantified using Genome Studio software (Illumina).
|
| Description |
4625016054_F
Ad8_DC
|
| Data processing |
Analysis of the iScan output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center (CGC) at http://www.vgtifl.org. Missing values were imputed using the KNN algorithm from the impute R package. Expression intensity filtering was performed keeping probe sets that have expression higher than log2(40) in at least 2 samples, Expression variability filtering was performed using the Inter Quartile Range (IQR) across the samples on the log2 is at least 0.3. Quantile normalization was applied, followed by a log2 transformation and differential gene expression testing using Limma from Bioconductor.
|
| |
|
| Submission date |
Nov 13, 2013 |
| Last update date |
Nov 01, 2014 |
| Contact name |
Peter A Wilkinson |
| Organization name |
Case Western Reserve University
|
| Department |
Pathology / Systems Biology & Bioinformatics
|
| Street address |
2103 Cornell Road
|
| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44120 |
| Country |
USA |
| |
|
| Platform ID |
GPL6883 |
| Series (1) |
| GSE52344 |
Myeloid Dendritic Cells Induce HIV-1 Latency in Non-Proliferating CD4+ T Cells |
|
