NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1122286 Query DataSets for GSM1122286
Status Public on May 02, 2014
Title iPS-derived neurons_HSV-1 quiescient infection 3
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: male
age (yrs): 48.7
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

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_19_P00315518 2.540827665
A_19_P00315519 2.538767584
A_19_P00315528 4.278697837
A_19_P00315529 5.578338627
A_19_P00315601 10.429781
A_19_P00315603 10.30890042
A_19_P00315625 2.819354696
A_19_P00315627 6.816441118
A_19_P00315631 2.63843685
A_19_P00315691 5.024682245
A_19_P00315810 7.462311366
A_19_P00315826 5.704061372
A_19_P00315841 4.690550627
A_19_P00315863 4.222067888
A_19_P00315905 2.477390056
A_19_P00315914 7.119125261
A_19_P00315936 8.52169826
A_19_P00315967 6.608235553
A_19_P00316035 2.94751732
A_19_P00316159 14.77053106

Total number of rows: 38804

Table truncated, full table size 957 Kbytes.




Supplementary file Size Download File type/resource
GSM1122286_HSV-1_quiescient_infection_3.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap