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Sample GSM678164 Query DataSets for GSM678164
Status Public on Jul 29, 2011
Title mRNA miR-7 1 (plier)
Sample type RNA
 
Source name HEY ovarian cancer cell, miR-7 mimic treated
Organism Homo sapiens
Characteristics originial tumor type of initial cell: Papillary Cystadenocarcinoma of the ovary
cell line: HEY
Biomaterial provider Gordon B. Mills
Treatment protocol Approximately 12h before transfection, these cells (1.5 × 105) were seeded on six-well plates in growth medium and allowed to adhere overnight at 37°C in a 5% CO2 atmosphere. The following day after washing the wells with PBS and replacing the growth medium with Opti-MEM (Invitrogen) cells were transfected with the miRNA [hsa-miR-7 miRIDIAN mimic, miRIDIAN miRNA mimic negative control #1 (miRNC), or has-miR-128 miRIDIAN mimic [(Thermo Fisher Scientific, Lafayette, CO)] using Lipofectamine 2000 transfection agent (Invitrogen) according to the manufacturer's instructions at a final concentration of 25nM. Cells were incubated for four hours, washed with PBS, and then incubated at 37°C and 5% CO2  for 44h (total 48h) after adding fresh growth medium to the wells.
Growth protocol Hey cells were cultured in RPMI 1640 (Mediatech, Manassas, VA) supplemented with 10% v/v heat-inactivated fetal calf serum (Invitrogen, Carlsbad, CA), 2 mM L-glutamine (Mediatech), 10 mM HEPES buffer (Mediatech), penicillin (100 U/ml), and streptomycin (100 μg/mL).
Extracted molecule total RNA
Extraction protocol RNA was isolated with Trizol (Invitrogen) and purified with PicoPure RNA Isolation Kit (Arcturus). RNA quality was verified on the Bioanalyzer RNA Pico Chip (Agilent Technologies).
Label biotin
Label protocol mRNAs were converted to double stranded (ds)-cDNA and amplified using Applause 3’-Amp System (NuGen, San Carlos, CA). This cDNA was then biotin labeled and fragmented by using Encode Biotin Module (NuGen)
 
Hybridization protocol Labeled mRNA was hybridized to GeneChip Human Genome U133 Plus 2.0 Arrays in the GeneChip Hybridization oven 640, further processed with the GeneChip Fluidics Station 450 and scanned with the GeneChip Scanner 3000.
Scan protocol as per manufacturer's protocol using GeneChip Scanner 3000.
Description HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.
Data processing PLIER via Affymetrix Expression Console (TM) Software Version 1.1. Fold change was calculated based on the log2 difference of average log2 signal values of samples calculated after this preprocessing step.
 
Submission date Feb 21, 2011
Last update date Jul 29, 2011
Contact name Shubin Shahab
E-mail(s) shubin.shahab@gmail.com
Organization name Georgia Institute of Technology
Department Biology
Lab McDonald
Street address 310 Ferst Drive
City Atlanta
State/province GA
ZIP/Postal code 30332
Country USA
 
Platform ID GPL570
Series (1)
GSE27431 miRNAs in ovarian cancer: A systems approach (MAS5, plier, GCRMA)

Data table header descriptions
ID_REF
VALUE Quantification

Data table
ID_REF VALUE
AFFX-BioB-5_at 1599
AFFX-BioB-M_at 2454.53
AFFX-BioB-3_at 2381.16
AFFX-BioC-5_at 3503.05
AFFX-BioC-3_at 3433.2
AFFX-BioDn-5_at 7990.77
AFFX-BioDn-3_at 10301.7
AFFX-CreX-5_at 15789
AFFX-CreX-3_at 14564
AFFX-DapX-5_at 22.9876
AFFX-DapX-M_at 3.75473
AFFX-DapX-3_at 18.8297
AFFX-LysX-5_at 12.3973
AFFX-LysX-M_at 46.7873
AFFX-LysX-3_at 4.94368
AFFX-PheX-5_at 6.70373
AFFX-PheX-M_at 8.40349
AFFX-PheX-3_at 20.3569
AFFX-ThrX-5_at 23.7242
AFFX-ThrX-M_at 8.98829

Total number of rows: 54675

Table truncated, full table size 1001 Kbytes.




Supplementary file Size Download File type/resource
GSM678164.CEL.gz 4.6 Mb (ftp)(http) CEL
GSM678164.chp.gz 396.1 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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