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Sample GSM343495 Query DataSets for GSM343495
Status Public on May 18, 2011
Title GFP-JTV-Alt Transfection - repeat 1 - mAdbID:75971
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: 1.89;; 2.41
Temperature: 35.57
Description mAdb experiment ID: 75971
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 0.677 1.598 1 1 1 7877 3414 114 140 5202 2165 210 240 0 0.677
1728380_1 0.532 1.446 1 1 2 6928 1902 107 89 5057 1412 208 108 0 0.532
1729712_1 0.695 1.619 1 1 3 2273 1071 131 95 1598 986 238 111 0 0.695
1730972_1 0.660 1 1 4 162 101 110 85 324 140 243 125 -50 -0.600
1732304_1 -0.871 0.547 1 1 5 237 130 104 74 509 97 259 128 0 -0.871
1733564_1 0.428 1 1 6 144 96 129 104 301 103 265 138 -50 -1.223
1734896_1 0.552 1 1 7 146 98 124 92 340 149 299 156 -50 -0.858
1736156_1 0.610 1.526 1 1 8 3121 975 138 122 2317 924 308 157 0 0.610
1737488_1 0.222 1.166 1 1 9 2174 883 142 120 2111 752 320 151 0 0.222
1738748_1 0.791 1 1 10 236 192 139 102 449 191 323 172 -50 -0.338
1740080_1 -0.695 0.618 1 1 11 470 145 163 108 836 230 325 174 0 -0.695
1741340_1 0.848 1 1 12 205 156 158 120 425 181 368 196 -50 -0.239
1742672_1 0.587 1 1 13 208 130 160 109 470 182 386 178 -50 -0.768
1743932_1 0.410 1.329 1 1 14 5954 2223 153 134 4884 1633 397 189 0 0.410
1745264_1 0.389 1.309 1 1 15 1178 660 155 117 1234 564 431 197 0 0.389
1746524_1 -0.159 0.896 1 1 16 608 252 153 133 919 301 397 205 0 -0.159
1747856_1 0.041 1 1 17 179 88 174 757 498 211 374 1022 -50 -4.593
1749116_1 -0.412 0.752 1 1 18 628 259 182 129 1021 325 411 257 0 -0.412
1750448_1 -0.421 0.747 1 1 19 6690 3702 169 110 9420 3968 446 213 0 -0.421
1751708_1 0.495 1.410 1 1 20 6093 1446 172 111 4724 1147 407 201 0 0.495

Total number of rows: 35024

Table truncated, full table size 2418 Kbytes.




Supplementary file Size Download File type/resource
GSM343495.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

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