NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM343497 Query DataSets for GSM343497
Status Public on May 18, 2011
Title GFP-JTV-Alt Transfection - repeat 2 - mAdbID:77133
Sample type RNA
 
Channel 1
Source name GFP-tranfected HeLa
Organism Homo sapiens
Characteristics cell line: HeLa tranfected with pEGFP-C1
Extracted molecule total RNA
Extraction protocol Sample Extraction Protocol
Extraction method: Trizol
Other: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) following manufacturer's protocol. Isopropanol precipitated RNA was further clarified by another ethanol precipitation.
Label cy3
Label protocol Cy3 Sample Labeling Protocol - generic
Other: Labeled using amino allyl conjugation method.
 
Channel 2
Source name GFP-JTV-Alt-tranfected HeLa
Organism Homo sapiens
Characteristics cell line: HeLa tranfected with pEGFP-JTV-Alt
Extracted molecule total RNA
Extraction protocol Sample Extraction Protocol
Extraction method: Trizol
Other: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) following manufacturer's protocol. Isopropanol precipitated RNA was further clarified by another ethanol precipitation.
Label cy5
Label protocol Cy5 Sample Labeling Protocol - generic
Other: Labeled using amino allyl conjugation method.
 
 
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 5.1.0.16
Scanner: GenePix 4000A [55478]
ScanPower: 100;; 100
LaserPower: 1.91;; 2.56
Temperature: 40.49
Description mAdb experiment ID: 77133
Data processing mAdb Data Processing Protocol (v. 1)
Calculation Method: 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 Nov 18, 2008
Last update date May 18, 2011
Contact name David Levens
E-mail(s) levens@helix.nih.gov
Phone 301-496-2176
Fax 301-402-0043
Organization name NIH
Department NCI/CCR
Lab LP
Street address 10 Center Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL3779
Series (1)
GSE13646 Global effect of JTV or JTV-Alt overexpression in HeLa cells

Data table header descriptions
ID_REF NCI mAdb well id plus replicate number
VALUE log2 of PRE_VALUE; log2 of (CY5 channel/CY3 channel) 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
UNF_VALUE log2 of PRE_VALUE; log2 of (CY5 channel/CY3 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 UNF_VALUE
1727120_1 1.049 2.068 1 1 1 32824 23220 123 64 18213 12604 214 115 0 1.049
1728380_1 0.844 1.796 1 1 2 19227 9349 155 420 12308 7225 215 170 0 0.844
1729712_1 0.486 1.401 1 1 3 7556 2248 124 59 6244 3409 204 366 0 0.486
1730972_1 -0.538 0.689 1 1 4 343 363 127 642 573 516 216 693 0 -0.538
1732304_1 -1.785 0.290 1 1 5 173 108 134 89 384 262 231 138 0 -1.785
1733564_1 -2.793 0.144 1 1 6 162 91 134 73 431 101 210 102 0 -2.793
1734896_1 -2.140 0.227 1 1 7 185 72 125 56 508 132 207 90 0 -2.140
1736156_1 0.914 1.884 1 1 8 15863 7930 130 56 9728 2920 219 118 0 0.914
1737488_1 0.664 1.585 1 1 9 5850 1712 130 64 4326 1896 217 112 0 0.664
1738748_1 -2.057 0.240 1 1 10 210 99 118 53 627 164 191 100 0 -2.057
1740080_1 0.274 1.209 1 1 11 1089 298 127 47 1107 491 201 150 0 0.274
1741340_1 0.056 1.039 1 1 12 307 294 118 51 390 107 183 98 0 0.056
1742672_1 -0.196 0.873 1 1 13 373 132 130 51 495 276 178 90 0 -0.196
1743932_1 -2.029 0.245 1 1 14 926 275 128 66 3908 860 201 204 0 -2.029
1745264_1 0.664 1.584 1 1 15 4275 1550 131 64 3158 1978 180 78 0 0.664
1746524_1 0.341 1.267 1 1 16 893 377 142 94 881 199 206 110 0 0.341
1747856_1 -0.150 0.901 1 1 17 403 189 133 77 553 254 212 139 0 -0.150
1749116_1 -0.682 0.623 1 1 18 255 170 128 61 428 294 196 147 0 -0.682
1750448_1 0.253 1.191 1 1 19 8847 3143 132 77 8515 3793 187 143 0 0.253
1751708_1 0.585 1.500 1 1 20 14312 6331 147 265 10948 5195 200 294 0 0.585

Total number of rows: 35024

Table truncated, full table size 2467 Kbytes.




Supplementary file Size Download File type/resource
GSM343497.gpr.gz 4.0 Mb (ftp)(http) GPR
Processed data included within Sample table
Raw data provided as supplementary file
Raw data included within Sample table

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