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Sample GSM1245962 Query DataSets for GSM1245962
Status Public on Oct 21, 2013
Title Hmeso MM line transfected with shCon, biological rep 2
Sample type RNA
Source name Stable transfection with shCon SureSilencing plasmid
Organism Homo sapiens
Characteristics cell line: epithelioid mesothelioma cell line HMESO
genotype/variation: control
Treatment protocol In order to obtain CREB inhibition human malignant mesothelioma cells were transfected with SureSilencing CREB1 plasmid (SuperArray Biosciences) using Lipofectamine 2000. After selecting for 15 days in G418 (400ug/ml) containing medium, limited dilution was performed to obtain clones showing ≥70% inhibition.
Growth protocol All cells were incubated at 37oC and 5% CO2 and grown to approximately 80-90% confluency in DMEM/F12 medium at a 1:1 ratio containing 10% fetal bovine serum (FBS), 0.1 ug/ml hydrocortisone, 2.5 ug/ml insulin, 2.5 ug/ml transferrin and 2.5 ng/ml sodium selenite and penicillin-streptomycin (50 U/ml penicillin G, 50 ug/ml streptomycin sulfate)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cells using an RNeasy Plus Mini kit according to the manufacturer's protocol (Qiagen, Valencia, CA). RNA was dissolved in RNAs free water and quantified using the NanoDrop spectrophotometer.
Label Biotin
Label protocol RNA was synthesized to ds cDNA which was then converted to amplified ss cDNA using a Nugen Ovation V2 system. ss cDNA was Biotinylated using TdT end label.
Hybridization protocol Biotin-labeled cDNA fragments that were hybridized to the probe array at 45 oC for 16 h.
Scan protocol The probe array were scanned (Affymetrix GeneArray Scanner, GS3000) to quantify the fluorescence intensity associated with each oligonucleotide probe
Description Gene expression data in epithelioid mesothelioma cell line transfected with shCon plasmid
Transfected MM lineERK1>70% inhibited
Data processing A human U133A 2.0 array was scanned twice, the images overlaid, and the average intensities of each probe cell compiled. Microarray data were analyzed using GeneSifter software (VizX Labs, Seattle, WA) by RMA method. Data were log transformed.
Submission date Oct 21, 2013
Last update date Oct 21, 2013
Contact name Arti Shukla
Phone 802-656-8253
Organization name University of Vermont
Department Pathology
Lab 215 HSRF
Street address 89 Beaumont Avenue
City Burlington
State/province VT
ZIP/Postal code 05405
Country USA
Platform ID GPL571
Series (1)
GSE51447 Microarray data from CREB inhibited and control mesothelioma cells

Data table header descriptions
VALUE RMA signal intensity, log transformed

Data table
1007_S_AT 8.89582
1053_AT 10.0249
117_AT 6.45419
121_AT 7.40181
1255_G_AT 2.92819
1294_AT 7.90244
1316_AT 8.56335
1320_AT 6.13227
1405_I_AT 8.44364
1431_AT 4.82881
1438_AT 5.7852
1487_AT 10.0304
1494_F_AT 5.33999
1598_G_AT 9.1795
160020_AT 8.84808
1729_AT 7.48528
1773_AT 6.22802
177_AT 6.71785
179_AT 8.37016
1861_AT 9.09055

Total number of rows: 22277

Table truncated, full table size 409 Kbytes.

Supplementary file Size Download File type/resource
GSM1245962_Hmeso-NC2-_21909-nugen_.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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