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Sample GSM1045805 Query DataSets for GSM1045805
Status Public on Dec 07, 2012
Title Differentiated SH-5Y cells (1) [mRNA]
Sample type RNA
Source name 24 hour treated with U937 media
Organism Homo sapiens
Characteristics cell line: neuronal cell line SH-SY5Y
treatment: mock
Treatment protocol Cells were treated for 24hrs with 0.1 pg/cell as calculated by p24 ELISA, of supernatant isolated from U-937-infected with HIV-1 JR-FL
Growth protocol Differentiated SH-SY5Y neuronal cell line (5 x 105) were grown in DMEM + 10% FBS on MatTek glass bottom plates treated with collagen (MatTek, Ashland, MA).
Extracted molecule total RNA
Extraction protocol Total RNA using Sureprep true total RNA isolation kit from Fisher scientific (#BP2800-50). RNA yield was measured on eppendorf biophotometer plus and 100 ng of total RNA was used as suggested by Affymetrix – GeneAtlas WT Expression kit manual. (Affymetrix, Santa Clara, CA), comprised of a total 33,297 probe sets.
Label Biotin
Label protocol Genechip WT terminal labeling kit (Affymetrix #901524) was used to label the DNA and Hybridize Affymetrix Human Gene 1.1 ST Array (#AF901626PR) using Accublock digital dry bath. Strips were washed and stained using kit (affymetrix #901667).
Hybridization protocol Genechip hybridization control kit (Affymetrix #900454) was used as requested and described by Affymetrix.
Scan protocol The scanner is the GeneAtlas scanner and the software control is GeneAtlas Instrument Control (GAIC) v. 1.0.6.
Description Differentiated SH-5Y cells, Mock 1
Data processing Quality control measures were carried out to ensure that RNA isolated was not degraded or lost. Housekeeping control genes and spike controls were routinely analyzed on the GeneAtlas® microarrays platform to confirm the successful labeling of target RNAs.
Two biological replicates were used and analysis was performed using Partek software and using RMA Statistical algorithm
GeneAtlas® array results were also correlated with the array design and annotation information using the NetAffxTM Analysis Center. Hierarchical cluster analysis and heat maps were generated using Spotfire DecisionSite 7.2.
Submission date Nov 29, 2012
Last update date Feb 12, 2013
Contact name Bassel E Sawaya
Phone 2157075446
Organization name Temple University
Department Neurology
Street address 3307 N. Broad Street
City Philadelphia
State/province PA
ZIP/Postal code 19140
Country USA
Platform ID GPL11532
Series (2)
GSE44265 HIV-1 Tat protein promotes neuronal dysfunction through disruption of microRNAs.
GSE44266 Deregulation of microRNAs by HIV-1 Vpr protein leads to the development of neurocognitive disorders.

Data table header descriptions
VALUE RMA signal

Data table
7892501 3.435353
7892502 4.675287
7892503 2.174451
7892504 6.58227
7892505 1.663758
7892506 2.997843
7892507 2.626736
7892508 5.588874
7892509 9.387623
7892510 5.295412
7892511 2.031133
7892512 3.038075
7892513 2.365453
7892514 10.12359
7892515 7.753233
7892516 2.286919
7892517 5.455077
7892518 1.970358
7892519 3.583196
7892520 8.292937

Total number of rows: 33297

Table truncated, full table size 549 Kbytes.

Supplementary file Size Download File type/resource 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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