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Sample GSM92090 Query DataSets for GSM92090
Status Public on Jan 26, 2006
Title HCC132 Cy3 - mAdbID:56978
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 HCC132 - Cy3
Organism Homo sapiens
Characteristics Gender: male
Age: 85
Tissue: liver
Developmental stage: adult
Cell type: Hepatocyte
Disease state: Hepatocellular carcinoma
Individual: HCC132
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: 56978
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 0.006 1.004 1 1 1 563 293 166 220 665 238 291 196 0
1174364_1 -0.478 0.718 1 1 2 2758 1026 174 587 3698 865 294 516 0
1175152_1 -0.503 0.706 1 1 3 267 250 176 656 410 266 288 515 -50
1175940_1 -0.209 0.865 1 1 4 1010 1751 183 522 1205 1659 301 524 0
1176716_1 -0.287 0.820 1 1 5 1100 1710 184 471 1357 2196 300 598 0
1177504_1 0.302 1.233 1 1 6 713 322 176 299 694 258 282 209 0
1178580_1 0.052 1.036 1 1 7 3125 1214 171 330 2976 1046 280 183 0
1179356_1 0.499 1.413 1 1 8 298 372 168 305 358 187 271 155 -50
1180144_1 0.245 1.185 1 1 9 477 344 165 206 524 247 275 123 0
1180932_1 1.050 2.071 1 1 10 470 521 181 271 395 154 263 158 0
1181708_1 0.483 1.397 1 1 11 331 263 167 235 378 213 267 205 -50
1182496_1 -0.273 0.828 1 1 12 216 231 174 209 318 190 270 200 -50
1183572_1 -0.598 0.661 1 1 13 479 290 187 272 692 182 274 174 0
1184348_1 -0.902 0.535 1 1 14 1189 1849 202 373 2047 3844 303 355 0
1185136_1 0.155 1.113 1 1 15 1144 1708 194 473 1096 1500 289 395 0
1185924_1 2.605 6.085 1 1 16 375 259 182 444 310 201 280 345 -50
1186700_1 -0.582 0.668 1 1 17 394 200 197 224 582 296 303 225 0
1187488_1 0.441 1.358 1 1 18 365 400 187 408 409 334 285 346 -50
1188564_1 -0.122 0.919 1 1 19 2646 943 176 438 2820 1017 278 535 0
1189340_1 -0.299 0.813 1 1 20 572 340 181 439 724 279 269 526 0

Total number of rows: 21794

Table truncated, full table size 1408 Kbytes.




Supplementary data files not provided

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