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Sample GSM92063 Query DataSets for GSM92063
Status Public on Jan 26, 2006
Title HCC119 Cy5 - mAdbID:56949
Sample type RNA
 
Channel 1
Source name Pooled Normal Liver Sample - Cy3
Organism Homo sapiens
Characteristics Tissue: liver
Developmental stage: adult
Cell type: Hepatocyte
Extracted molecule total RNA
Extraction protocol CsCl Extraction Protocol
Extraction method: ultracentrifugation
Label cy3
Label protocol Cy3 Sample Labeling Protocol - generic
 
Channel 2
Source name HCC119 - Cy5
Organism Homo sapiens
Characteristics Gender: female
Age: 81
Tissue: liver
Developmental stage: adult
Cell type: Hepatocyte
Disease state: Hepatocellular carcinoma
Individual: HCC119
Extracted molecule total RNA
Extraction protocol CsCl Extraction Protocol
Extraction method: ultracentrifugation
Label cy5
Label protocol Cy5 Sample Labeling Protocol - generic
 
 
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")
Description mAdb experiment ID: 56949
Data processing After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.
 
Submission date Jan 12, 2006
Last update date Jan 26, 2006
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)
GSE4024 HCC Gene Expression Profile

Data table header descriptions
ID_REF NCI mAdb well id plus replicate number
VALUE log ratio (log2 of PRE_VALUE)
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

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
1173588_1 -0.169 0.890 1 1 1 253 119 184 146 250 78 179 227 -50
1174364_1 0.274 1.209 1 1 2 15250 2937 191 205 11580 2811 181 81 0
1175152_1 0.346 1.271 1 1 3 534 281 187 331 435 242 185 178 0
1175940_1 0.108 1.078 1 1 4 1598 678 184 346 1389 918 188 342 0
1176716_1 0.364 1.287 1 1 5 1871 507 184 103 1375 492 175 270 0
1177504_1 0.454 1.370 1 1 6 2917 622 184 128 2003 415 177 225 0
1178580_1 0.713 1.639 1 1 7 56291 12573 199 268 31504 6436 176 188 0
1179356_1 0.393 1.313 1 1 8 490 183 186 148 382 153 170 158 0
1180144_1 -1.549 0.342 1 1 9 421 289 191 182 795 404 179 120 0
1180932_1 0.098 1.071 1 1 10 476 283 186 183 431 304 183 233 0
1181708_1 -0.739 0.599 1 1 11 395 155 179 236 494 214 164 218 0
1182496_1 -0.162 0.894 1 1 12 216 88 175 233 208 88 166 186 -50
1183572_1 -0.097 0.935 1 1 13 1287 354 180 233 1266 416 182 109 0
1184348_1 0.187 1.138 1 1 14 336 147 203 175 296 100 189 88 0
1185136_1 0.525 1.439 1 1 15 297 449 187 216 252 339 182 194 -50
1185924_1 -0.261 0.835 1 1 16 354 174 189 549 361 209 180 367 0
1186700_1 0.697 1.622 1 1 17 783 356 179 532 515 234 174 342 0
1187488_1 2.386 5.229 1 1 18 963 2699 192 237 318 210 183 107 0
1188564_1 -0.517 0.699 1 1 19 3596 1395 198 199 4631 1364 178 91 0
1189340_1 -0.015 0.990 1 1 20 663 173 197 158 603 211 172 85 0

Total number of rows: 21794

Table truncated, full table size 1380 Kbytes.




Supplementary data files not provided

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