|
| Status |
Public on May 02, 2014 |
| Title |
iPS-derived neurons_HSV-1 quiescient infection 1 |
| Sample type |
RNA |
| |
|
| Source name |
iPS-derived neurons_HSV-1 quiescient infection
|
| Organism |
Homo sapiens |
| Characteristics |
tissue source: human skin biopsy samples
cells: glutamatergic neurons
cell type: human iPS-derived neurons
gender: female
age (yrs): 29.0
|
| Treatment protocol |
Neuronal cultures were either infected with HSV-1 in triplicate or uninfected, with each individual sample harvested separately to provide biological replicates for expression analysis. Microarray analysis was performed on i) uninfected neurons; ii) neurons infected with HSV-1 at an MOI of 0.3 in the presence or absence of (E)-5-(2-bromovinyl)-2'-deoxyuridine along with interferon (IFN)-α; iii) neuron quiescent cultures treated with sodium butyrate (NaB, 5 mM); iv) uninfected neurons treated with E)-5-(2-bromovinyl)-2'-deoxyuridine and interferon IFN-α; v) uninfected neurons treated with NaB
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy kits (Qiagen)
|
| Label |
Cy3-CTP
|
| Label protocol |
Cy3-CTP labeled RNA was prepared according to the standard Agilent protocol from 50ng total RNA.
|
| |
|
| Hybridization protocol |
Labeled RNA was hybridized for 17 hr at 65C on Agilent gene expression array. Arrays were washed according to the manufacturer's protocol.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8X60K array slides
|
| Description |
iPS-derived neurons
|
| Data processing |
Agilent Feature Extraction v10.7.3.1 default parameters and further analyzed by a cyclic loess algorithm authored in the R programming environment using the Bioconductor suite of tools, and only probes with Entrez gene IDs are selected for further analysis (in total 38804).
|
| |
|
| Submission date |
Apr 15, 2013 |
| Last update date |
May 02, 2014 |
| Contact name |
Leonardo D'Aiuto |
| E-mail(s) |
daiutol@upmc.edu
|
| Phone |
4126570558
|
| Organization name |
UPMC
|
| Street address |
3811 O’Hara Street
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
|
| Platform ID |
GPL17077 |
| Series (2) |
| GSE46041 |
Human cellular models for Herpes Simplex Virus, type 1 (HSV-1) using induced pluripotent stem cell derived neuronal lineages |
| GSE46043 |
Induced pluripotent stem cell derived neuronal lineages as human cellular models for Herpes Simplex Virus, type 1 (HSV-1) infections |
|
