|
| Status |
Public on Aug 04, 2009 |
| Title |
CN - cy3 (144) - repeat 36 - mAdbID:73878 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Pooled Normal Liver - cy5
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue: liver
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA Easy Mini Kit Extraction
Other: Total RNA isolation together with the DNase digestion was performed with the RNA Easy Mini kit (Qiagen, Valencia, CA) following the manufacturer recommendations. Approximately one ìg of total RNA was reversed transcribed and linearly amplified with the Aminoallyl MessageAmp II kit (Ambion, Austin, TX) according to the included protocol.
|
| Label |
cy5
|
| Label protocol |
Cy5 Sample Labeling Protocol
Other: Two ug of the aminoallyl-UTP modified aRNA product was indirectly labeled with Cy5 fluorescent dye.
|
| |
|
| Channel 2 |
| Source name |
CN - cy3
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue: liver
Disease state: Regenerative (cirrhotic) nodules
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA Easy Mini Kit Extraction
Other: Total RNA isolation together with the DNase digestion was performed with the RNA Easy Mini kit (Qiagen, Valencia, CA) following the manufacturer recommendations. Approximately one ìg of total RNA was reversed transcribed and linearly amplified with the Aminoallyl MessageAmp II kit (Ambion, Austin, TX) according to the included protocol.
|
| Label |
cy3
|
| Label protocol |
Cy3 Sample Labeling Protocol
Other: Two ug of the aminoallyl-UTP modified aRNA product was indirectly labeled with Cy3 fluorescent dye.
|
| |
|
| |
| Hybridization protocol |
NCI Oligo Microarray Hybridization
Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")
|
| Scan protocol |
Creator: GenePix Pro 5.1.0.11
Scanner: GenePix 4000A [54243]
ScanPower: 100;; 100
LaserPower: 2.53;; 1.54
Temperature: 40.93
|
| Description |
mAdb experiment ID: 73878
|
| Data processing |
mAdb Data Processing Protocol (v. 2)
Calculation Method: After background correction, ratios were median centered based on signals greater than 100 in both channels and linear transformed to obtain the log and linear values given in the data table.
|
| |
|
| Submission date |
Aug 14, 2008 |
| Last update date |
Aug 04, 2009 |
| Contact name |
Snorri S Thorgeirsson |
| E-mail(s) |
snorri_s_thorgeirsson@nih.gov
|
| Phone |
(301) 496-5688 x204
|
| Fax |
(301) 496-0734
|
| URL |
http://neoplasia.nci.nih.gov/
|
| Organization name |
National Cancer institute/NIH
|
| Department |
Laboratory of Experimental Carcinogenesis
|
| Lab |
Cellular and Molecular Biology Section
|
| Street address |
37 Convent Dr. # 4146
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL1528 |
| Series (1) |
| GSE12443 |
The Central Role of c-Myc during Malignant Conversion in Human Hepatocarcinogenesis |
|
| Data table header descriptions |
| ID_REF |
NCI mAdb well id plus replicate number |
| VALUE |
same as UNF_VALUE but with flagged values removed |
| PRE_VALUE |
Calibrated Ratio (CY5 channel/CY3 channel) |
| Slide_block |
Array block location |
| Slide_column |
Array column location |
| Slide_row |
Array row location |
| CY5_mean |
Red Channel Sample mean Signal (Background Subtracted) |
| CY5_SD |
Red Channel Sample Standard Deviation |
| CY5_BKD_median |
Red Channel Sample median Background Level |
| CY5_BKD_SD |
Red Channel Sample Background Standard Deviation |
| CY3_mean |
Green Channel Sample mean Signal (Background Subtracted) |
| CY3_SD |
Green Channel Sample Standard Deviation |
| CY3_BKD_median |
Green Channel Sample median Background Level |
| CY3_BKD_SD |
Green Channel Sample Background Standard Deviation |
| Flag |
Quality flag 0->good, -50->Not found, -100->Bad |
| INV_VALUE |
log ratio (log2 of PRE_VALUE) |
| UNF_VALUE |
log2 ratio of (CY3 channel/CY5 channel) |
