|
Status |
Public on Sep 29, 2012 |
Title |
OVCAR 5009 IRES R1 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
Stratagene Mouse Universal Reference
|
Organism |
Mus musculus |
Characteristics |
reference: Mouse Reference
|
Biomaterial provider |
Stratagene
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA isolated by Stratagene
|
Label |
Cy3
|
Label protocol |
Agilent
|
|
|
Channel 2 |
Source name |
Cell line generated in the Blancafort Lab
|
Organism |
Mus musculus |
Characteristics |
cell line: Ovarian MOVCAR 5009 treatment: none
|
Extracted molecule |
total RNA |
Extraction protocol |
Qiagen Rneasy Kit
|
Label |
Cy5
|
Label protocol |
Agilent
|
|
|
|
Hybridization protocol |
Agilent
|
Scan protocol |
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.
|
Description |
Mouse Ovarian Cell Line:MOVCAR 5009 Control R1
|
Data processing |
Data for both channels were Lowess-normalized and then log(2) ratio was taken
|
|
|
Submission date |
Mar 08, 2012 |
Last update date |
Sep 29, 2012 |
Contact name |
PILAR BLANCAFORT |
E-mail(s) |
pilar_blancafort@med.unc.edu
|
Phone |
919-966-1615
|
Fax |
919-966-5640
|
Organization name |
UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL
|
Department |
PHARMACOLOGY
|
Lab |
BLANCAFORT
|
Street address |
4009 MASON FARM RD
|
City |
CHAPEL HILL |
State/province |
NORTH CAROLINA |
ZIP/Postal code |
27599 |
Country |
USA |
|
|
Platform ID |
GPL11383 |
Series (1) |
GSE36396 |
Targeting serous epithelial ovarian cancer with designer zinc finger transcription factors |
|
Data table header descriptions |
ID_REF |
Spot Reference ID |
VALUE |
log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_MEAN) |
SPOT |
spot number on array |
CH1_MEAN |
|
CH1_SD |
standard deviation of channel 1 intensity |
CH1_BKD_MEDIAN |
channel 1 background median intensity |
CH1_BKD_SD |
standard deviation of channel 1 background median intensity |
CH2_MEAN |
channel 2 mean intensity |
CH2_SD |
standard deviation of channel 2 intensity |
CH2_BKD_MEDIAN |
channel 2 background median intensity |
CH2_BKD_SD |
standard deviation of channel 2 background median intensity |
TOT_BPIX |
number of background pixels |
TOT_SPIX |
number of spot pixels |
CH2BN_MEDIAN |
channel 2 normalized background median intensity |
CH2IN_MEAN |
channel 2 normalized mean intensity |
CH1DL_MEAN |
channel 1 Lowess_normalized mean intensity |
CH2DL_MEAN |
channel 2 Lowess_normalized mean intensity |
LOG_RAT2N_MEAN |
log2_ratio of channel 2 normalized over channel 1 (global normalization) |
CORR |
correlation coefficient among pixels |
FLAG |
Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots |