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Sample GSM1245968 Query DataSets for GSM1245968
Status Public on Oct 21, 2013
Title Mill MM line transfected with shCREB1, biological rep 2
Sample type RNA
Source name Stable transfection with shCREB1 SureSilencing plasmid
Organism Homo sapiens
Characteristics cell line: fibrosarcomatoid mesothelioma cell line H2373/PPMMill
genotype/variation: CREB inhibition
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 CREB1 inhibited fibrosarcomatoid mesothelioma cell line
CREB1>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 9.31214
1053_AT 9.00058
117_AT 8.14345
121_AT 7.61825
1255_G_AT 3.04123
1294_AT 8.25958
1316_AT 9.42583
1320_AT 6.3483
1405_I_AT 7.39786
1431_AT 4.94314
1438_AT 5.80495
1487_AT 10.5284
1494_F_AT 5.35105
1598_G_AT 10.0998
160020_AT 10.0009
1729_AT 8.11928
1773_AT 6.20425
177_AT 7.76076
179_AT 8.4928
1861_AT 9.21552

Total number of rows: 22277

Table truncated, full table size 409 Kbytes.

Supplementary file Size Download File type/resource
GSM1245968_Mill-Creb-35.2-_21909-nugen_.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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