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Sample GSM312589 Query DataSets for GSM312589
Status Public on Aug 04, 2009
Title CN - cy3 (2) - repeat 34 - mAdbID:73196
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: 2.41;; 1.63
Temperature: 35.75
Description mAdb experiment ID: 73196
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)

Data table
ID_REF VALUE PRE_VALUE Slide_block Slide_column Slide_row CY5_mean CY5_SD CY5_BKD_median CY5_BKD_SD CY3_mean CY3_SD CY3_BKD_median CY3_BKD_SD Flag INV_VALUE UNF_VALUE
1174261_1 -0.136 1.099 1 1 2 240 58 49 14 294 42 116 16 0 0.136 -0.136
1175033_1 -0.091 1.065 1 1 3 153 41 50 15 216 40 117 16 0 0.091 -0.091
1175841_1 -0.012 1.008 1 1 4 303 112 51 16 372 88 116 17 0 0.012 -0.012
1176613_1 0.286 0.820 1 1 5 239 66 50 14 353 241 117 16 0 -0.286 0.286
1177385_1 0.178 0.884 1 1 6 1931 633 50 15 2297 628 118 17 0 -0.178 0.178
1179253_1 0.108 0.928 1 1 8 1104 323 49 14 1276 358 112 16 0 -0.108 0.108
1180025_1 -0.485 1.400 1 1 9 839 202 49 14 690 142 112 16 0 0.485 -0.485
1180833_1 -0.182 1.134 1 1 10 2959 1111 49 14 2737 943 110 16 0 0.182 -0.182
1181605_1 0.095 0.936 1 1 11 432 96 48 19 530 82 110 43 0 -0.095 0.095
1182377_1 -0.074 1.053 1 1 12 1669 372 48 14 1686 285 109 18 0 0.074 -0.074
1184245_1 0.175 0.886 1 1 14 193 56 46 13 278 48 108 15 0 -0.175 0.175
1185017_1 0.317 0.803 1 1 15 76 22 47 13 145 21 108 15 0 -0.317 0.317
1185825_1 -0.023 1.016 1 1 16 306 80 48 15 370 58 110 16 0 0.023 -0.023
1186597_1 -0.105 1.075 1 1 17 1161 322 48 16 1170 271 110 17 0 0.105 -0.105
1187369_1 -0.35 1.274 1 1 18 156 45 49 13 196 38 110 16 0 0.350 -0.35
1189237_1 0.437 0.738 1 1 20 156 39 50 15 258 42 111 16 0 -0.437 0.437
1190009_1 0.179 0.884 1 1 21 95 24 51 14 163 26 112 16 0 -0.179 0.179
1190817_1 -0.087 1.062 1 1 22 749 146 51 16 787 125 114 15 0 0.087 -0.087
1191589_1 -0.094 1.068 1 1 23 147 30 49 16 209 32 115 16 0 0.094 -0.094
1192361_1 0.295 0.815 1 1 24 88 23 49 16 162 25 113 16 0 -0.295 0.295

Total number of rows: 21777

Table truncated, full table size 1584 Kbytes.




Supplementary file Size Download File type/resource
GSM312589.gpr.gz 2.4 Mb (ftp)(http) GPR
Processed data included within Sample table

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