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Sample GSM312626 Query DataSets for GSM312626
Status Public on Aug 04, 2009
Title CN - cy3 (146) - repeat 48 - mAdbID:73874
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: 2.52;; 1.36
Temperature: 39.48
Description mAdb experiment ID: 73874
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 -0.585 1.500 1 1 2 212 50 83 36 367 97 296 67 0 0.585 -0.585
1175033_1 -1.216 2.324 1 1 3 158 72 82 39 339 101 312 66 0 1.216 -1.216
1175841_1 0.64 0.642 1 1 4 350 72 81 44 643 117 297 58 0 -0.640 0.64
1176613_1 -0.782 1.720 1 1 5 255 75 80 37 375 91 291 53 0 0.782 -0.782
1177385_1 0.446 0.734 1 1 6 2076 918 75 27 2538 1040 288 53 0 -0.446 0.446
1179253_1 -1 1.999 1 1 8 708 675 71 33 550 342 287 59 0 1.000 -1
1180025_1 0.298 0.813 1 1 9 404 162 73 31 614 196 278 54 0 -0.298 0.298
1180833_1 1.175 0.443 1 1 10 2354 1107 75 28 4532 2133 285 72 0 -1.175 1.175
1181605_1 6.810 1 1 11 140 57 74 37 291 70 283 67 -50 2.768 -2.768
1182377_1 0.559 0.679 1 1 12 929 279 74 32 1326 340 286 66 0 -0.559 0.559
1184245_1 0.431 1 1 14 84 25 72 95 309 54 286 65 -50 -1.215 1.215
1185017_1 12.382 1 1 15 83 33 68 31 278 55 281 67 -50 3.630 -3.63
1185825_1 -0.348 1.273 1 1 16 270 48 68 54 412 83 281 81 0 0.348 -0.348
1186597_1 0.802 0.574 1 1 17 1604 470 68 50 2494 702 284 60 0 -0.802 0.802
1187369_1 17.335 1 1 18 88 25 67 23 276 50 275 55 -50 4.116 -4.116
1189237_1 1.366 0.388 1 1 20 105 44 66 27 359 64 276 48 0 -1.366 1.366
1190009_1 0.250 1 1 21 76 26 66 27 311 62 278 59 -50 -1.999 1.999
1190817_1 -0.045 1.032 1 1 22 3209 1219 65 23 2796 1039 281 57 0 0.045 -0.045
1191589_1 3.715 1 1 23 92 34 65 23 278 64 272 55 -50 1.893 -1.893
1192361_1 0.571 1 1 24 94 33 67 30 309 60 270 59 -50 -0.807 0.807

Total number of rows: 21777

Table truncated, full table size 1544 Kbytes.




Supplementary file Size Download File type/resource
GSM312626.gpr.gz 2.4 Mb (ftp)(http) GPR
Processed data included within Sample table

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