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Sample GSM312624 Query DataSets for GSM312624
Status Public on Aug 04, 2009
Title CN - cy3 (145) - repeat 46 - mAdbID:73872
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: 2.51;; 1.41
Temperature: 38.36
Description mAdb experiment ID: 73872
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 1.416 0.375 1 1 2 243 55 57 33 699 1913 267 44 0 -1.416 1.416
1175033_1 -0.435 1.351 1 1 3 164 44 60 56 335 65 268 73 0 0.435 -0.435
1175841_1 0.273 0.828 1 1 4 251 111 59 39 473 176 271 54 0 -0.273 0.273
1176613_1 -1.003 2.005 1 1 5 256 77 58 64 354 135 268 48 0 1.003 -1.003
1177385_1 0.518 0.698 1 1 6 1640 962 57 27 2237 1793 263 48 0 -0.518 0.518
1179253_1 -0.117 1.084 1 1 8 706 391 56 31 780 552 258 52 0 0.117 -0.117
1180025_1 -0.428 1.346 1 1 9 515 279 56 212 555 219 258 72 0 0.428 -0.428
1180833_1 1.315 0.402 1 1 10 2253 1225 57 215 5008 2540 252 50 0 -1.315 1.315
1181605_1 -1.759 3.385 1 1 11 370 107 59 67 338 67 258 69 0 1.759 -1.759
1182377_1 0.008 0.995 1 1 12 1135 384 53 69 1211 406 264 67 0 -0.008 0.008
1184245_1 0.697 1 1 14 97 34 45 25 306 59 241 47 -50 -0.522 0.522
1185017_1 1.524 1 1 15 62 28 48 30 256 43 248 48 -50 0.608 -0.608
1185825_1 -0.584 1.499 1 1 16 351 103 48 31 432 118 256 46 0 0.584 -0.584
1186597_1 0.751 0.594 1 1 17 703 321 49 28 1217 468 259 51 0 -0.751 0.751
1187369_1 15.672 1 1 18 68 34 50 32 239 41 257 48 -50 3.970 -3.97
1189237_1 28.732 1 1 20 84 34 51 27 253 44 263 49 -50 4.845 -4.845
1190009_1 0.871 1 1 21 51 16 53 33 259 52 263 54 -50 -0.200 0.2
1190817_1 0.114 0.924 1 1 22 728 178 50 32 896 192 257 52 0 -0.114 0.114
1191589_1 6.095 1 1 23 57 19 50 31 239 45 260 49 -50 2.608 -2.608
1192361_1 6.095 1 1 24 56 18 49 30 238 42 261 46 -50 2.608 -2.608

Total number of rows: 21777

Table truncated, full table size 1549 Kbytes.




Supplementary file Size Download File type/resource
GSM312624.gpr.gz 2.4 Mb (ftp)(http) GPR
Processed data included within Sample table

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