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Sample GSM542318 Query DataSets for GSM542318
Status Public on May 08, 2010
Title MM line transfected with shCon, rep1
Sample type RNA
Source name Stable transfection with shCon SureSilencing plasmid
Organism Homo sapiens
Characteristics cell line: HMESO
cell type: epithelioid malignant mesothelioma (MM)
transfection: shControl
Treatment protocol In order to achieve inhibition of ERK1 or ERK2, mesothelioma cells (HMESO) were stably transfected with either shControl, shERK1 or shERK2 plasmid from SABiosciences using Lipofectamine 2000. After selection in G418 (400ug/ml) medium for 14 days, limited dilution was performed to get pure clones of more than 70% inhibited ERK1 or ERK2.
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 RNAse-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 were hybridized to the probe array at 45oC 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.
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 the RMA method. Data were log transformed.
Submission date May 07, 2010
Last update date May 07, 2010
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)
GSE21750 Expression data from mesothelial (LP9) and mesothelioma cells (HMESO) inhibited for extracellular-regulated kinase (ERK) 1, 2, or 5

Data table header descriptions
VALUE RMA signal intensity, log transformed

Data table
1007_S_AT 10.4641
1053_AT 11.1573
117_AT 8.21579
121_AT 7.54249
1255_G_AT 3.36696
1294_AT 8.42282
1316_AT 8.71577
1320_AT 6.05124
1405_I_AT 9.25053
1431_AT 4.54832
1438_AT 5.74201
1487_AT 10.3885
1494_F_AT 4.96923
1598_G_AT 10.7337
160020_AT 9.27661
1729_AT 8.59887
1773_AT 6.48124
177_AT 7.75606
179_AT 7.84094
1861_AT 9.00783

Total number of rows: 22277

Table truncated, full table size 409 Kbytes.

Supplementary file Size Download File type/resource
GSM542318.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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