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Sample GSM92142 Query DataSets for GSM92142
Status Public on Jan 26, 2006
Title HCC103 Cy3 - mAdbID:59865
Sample type RNA
 
Channel 1
Source name Pooled Normal Liver Sample - Cy5
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 cy5
Label protocol Cy5 Sample Labeling Protocol - generic
 
Channel 2
Source name HCC103 - Cy3
Organism Homo sapiens
Characteristics Gender: male
Age: 64
Tissue: liver
Developmental stage: adult
Cell type: Hepatocyte
Disease state: Hepatocellular carcinoma
Individual: HCC103
Extracted molecule total RNA
Extraction protocol CsCl Extraction Protocol
Extraction method: ultracentrifugation
Label cy3
Label protocol Cy3 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: 59865
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 -0.081 0.946 1 1 1 3443 1990 121 179 3608 2258 346 849 0
1174364_1 -0.083 0.944 1 1 2 13055 6448 122 148 13071 6208 348 684 0
1175152_1 0.343 1.269 1 1 3 1748 424 133 150 1540 390 358 612 0
1175940_1 0.315 1.244 1 1 4 1174 302 128 142 1153 216 372 600 0
1176716_1 -0.360 0.779 1 1 5 6822 2867 124 114 8358 2469 378 487 0
1177504_1 0.172 1.127 1 1 6 2811 525 134 161 2589 540 383 490 0
1178580_1 0.530 1.444 1 1 7 19578 4171 139 142 12887 3190 387 820 0
1179356_1 0.277 1.212 1 1 8 1926 396 139 137 1725 352 356 559 0
1180144_1 -0.725 0.605 1 1 9 1493 263 136 141 2443 605 361 619 0
1180932_1 -0.170 0.889 1 1 10 1358 652 127 187 1625 591 339 493 0
1181708_1 -0.230 0.853 1 1 11 432 193 129 238 661 257 331 408 0
1182496_1 0.204 1.152 1 1 12 552 152 145 271 745 200 417 934 0
1183572_1 -0.285 0.821 1 1 13 2348 511 144 230 2860 536 366 689 0
1184348_1 -0.599 0.660 1 1 14 399 252 133 218 739 466 365 529 0
1185136_1 -1.732 0.301 1 1 15 215 153 132 176 666 452 410 612 0
1185924_1 -0.328 0.797 1 1 16 1064 309 141 148 1453 656 377 567 0
1186700_1 -0.188 0.878 1 1 17 5038 1403 145 307 5562 1462 386 798 0
1187488_1 -0.627 0.648 1 1 18 771 227 146 211 1263 311 367 684 0
1188564_1 0.202 1.150 1 1 19 5745 1193 155 230 4891 896 379 778 0
1189340_1 0.025 1.018 1 1 20 2269 445 136 227 2346 504 400 914 0

Total number of rows: 21777

Table truncated, full table size 1409 Kbytes.




Supplementary data files not provided

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