NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1122290 Query DataSets for GSM1122290
Status Public on May 02, 2014
Title iPS-derived neurons_uninfected + 5BVdU + IFN-alpha 1
Sample type RNA
 
Source name iPS-derived neurons_uninfected + 5BVdU + IFN-alpha
Organism Homo sapiens
Characteristics tissue source: human skin biopsy samples
cells: glutamatergic neurons
cell type: human iPS-derived neurons
gender: male
age (yrs): 24.2
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 2.523740741
A_19_P00315519 3.382121254
A_19_P00315528 3.319979106
A_19_P00315529 3.31687034
A_19_P00315601 9.692038452
A_19_P00315603 9.601398165
A_19_P00315625 3.509493345
A_19_P00315627 7.173612091
A_19_P00315631 2.67788768
A_19_P00315691 4.769064886
A_19_P00315810 6.930922379
A_19_P00315826 4.69720053
A_19_P00315841 4.427723065
A_19_P00315863 2.761218753
A_19_P00315905 2.456758136
A_19_P00315914 6.415038813
A_19_P00315936 7.954820386
A_19_P00315967 5.638304008
A_19_P00316035 4.312763266
A_19_P00316159 16.90702936

Total number of rows: 38804

Table truncated, full table size 957 Kbytes.




Supplementary file Size Download File type/resource
GSM1122290_uninfected_+_5BVdU_+_IFN-alpha_1.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