NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM312582 Query DataSets for GSM312582
Status Public on Aug 04, 2009
Title CN - cy3 (17) - repeat 16 - mAdbID:73184
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: 2.4;; 1.6
Temperature: 33.17
Description mAdb experiment ID: 73184
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 -0.302 1.233 1 1 2 897 251 55 18 789 226 97 17 0 0.302 -0.302
1175033_1 -0.123 1.089 1 1 3 343 77 56 18 364 78 97 15 0 0.123 -0.123
1175841_1 0.039 0.974 1 1 4 1999 627 56 19 2119 676 97 16 0 -0.039 0.039
1176613_1 -0.383 1.304 1 1 5 727 255 55 18 617 215 95 16 0 0.383 -0.383
1177385_1 0.263 0.833 1 1 6 4472 1434 53 17 5463 2024 90 25 0 -0.263 0.263
1179253_1 -0.051 1.036 1 1 8 2596 1220 52 18 2581 983 94 17 0 0.051 -0.051
1180025_1 -0.876 1.835 1 1 9 1863 777 52 24 1097 373 97 25 0 0.876 -0.876
1180833_1 0.49 0.712 1 1 10 8323 3407 54 20 11861 4043 96 20 0 -0.490 0.49
1181605_1 -0.484 1.399 1 1 11 648 125 53 41 527 128 96 22 0 0.484 -0.484
1182377_1 -0.045 1.032 1 1 12 4466 2171 54 21 4426 1799 94 19 0 0.045 -0.045
1184245_1 0.132 0.912 1 1 14 328 78 56 21 397 96 95 19 0 -0.132 0.132
1185017_1 -0.108 1.077 1 1 15 190 78 56 27 220 61 94 21 0 0.108 -0.108
1185825_1 -0.429 1.346 1 1 16 806 172 54 21 661 145 95 19 0 0.429 -0.429
1186597_1 0.198 0.872 1 1 17 5134 1181 55 22 5996 1169 94 17 0 -0.198 0.198
1187369_1 -0.252 1.191 1 1 18 276 85 55 27 282 49 94 16 0 0.252 -0.252
1189237_1 -0.086 1.062 1 1 20 358 80 52 21 386 65 94 18 0 0.086 -0.086
1190009_1 0.036 0.975 1 1 21 780 268 54 21 850 204 96 41 0 -0.036 0.036
1190817_1 -0.14 1.102 1 1 22 4817 1342 57 24 4477 894 101 41 0 0.140 -0.14
1191589_1 -0.773 1.709 1 1 23 275 71 54 20 226 36 95 18 0 0.773 -0.773
1192361_1 -0.001 1.001 1 1 24 300 80 54 22 345 85 96 24 0 0.001 -0.001

Total number of rows: 21777

Table truncated, full table size 1551 Kbytes.




Supplementary file Size Download File type/resource
GSM312582.gpr.gz 2.3 Mb (ftp)(http) GPR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap