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Sample GSM1020015 Query DataSets for GSM1020015
Status Public on Oct 15, 2012
Title MM line transfected with shERK5, rep 2
Sample type RNA
Source name Stable transfection with shERK5 SureSilencing plasmid
Organism Homo sapiens
Characteristics cell line: HMESO
cell type: epithelioid malignant mesothelioma (MM)
transfection: shERK5
property: ERK5>70% inhibited
Treatment protocol In order to achieve inhibition of ERK5, mesothelioma cells (HMESO) were stably transfected with shERK5 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 ERK5.
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 ERK5 inhibited epithelioid mesothelioma cell line
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 15, 2012
Last update date Oct 15, 2012
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 10.3024
1053_AT 11.1826
117_AT 6.24164
121_AT 8.13692
1255_G_AT 3.11558
1294_AT 8.21256
1316_AT 9.24247
1320_AT 5.63309
1405_I_AT 5.99594
1431_AT 4.52505
1438_AT 5.78374
1487_AT 10.2644
1494_F_AT 5.25065
1598_G_AT 12.5236
160020_AT 9.73766
1729_AT 8.93631
1773_AT 6.43915
177_AT 7.90714
179_AT 8.00687
1861_AT 9.0964

Total number of rows: 22277

Table truncated, full table size 409 Kbytes.

Supplementary file Size Download File type/resource
GSM1020015_23-Hmeso-ERK5-2-_NuGEN-40ng_-Shukla-121608-23.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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