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Sample GSM343496 Query DataSets for GSM343496
Status Public on May 18, 2011
Title GFP-JTV Transfection - repeat 2 - mAdbID:77132
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-tranfected HeLa
Organism Homo sapiens
Characteristics cell line: HeLa tranfected with pEGFP-JTV
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: 1.9;; 2.2
Temperature: 40.17
Description mAdb experiment ID: 77132
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 1.217 2.324 1 1 1 36211 13773 133 139 19276 7291 190 218 0 1.217
1728380_1 0.998 1.997 1 1 2 17236 5675 157 101 10697 5853 183 137 0 0.998
1729712_1 0.794 1.734 1 1 3 4627 3988 128 74 3359 2878 169 108 0 0.794
1730972_1 1.043 2.060 1 1 4 486 212 124 130 384 105 168 125 0 1.043
1732304_1 -0.295 0.815 1 1 5 247 188 133 69 356 177 184 146 0 -0.295
1733564_1 -0.376 0.771 1 1 6 216 98 127 74 358 332 216 129 0 -0.376
1734896_1 0.766 1 1 7 169 88 136 179 222 120 169 135 -50 -0.386
1736156_1 1.459 2.750 1 1 8 16130 1406 119 69 7323 3263 164 112 0 1.459
1737488_1 0.685 1.608 1 1 9 5730 1154 135 174 4433 2237 154 132 0 0.685
1738748_1 1.483 1 1 10 224 132 148 146 245 126 182 133 -50 0.569
1740080_1 0.373 1.295 1 1 11 894 293 128 110 920 454 193 140 0 0.373
1741340_1 0.050 1.035 1 1 12 354 731 125 90 453 212 181 155 0 0.050
1742672_1 -0.079 0.946 1 1 13 411 222 110 83 549 172 158 131 0 -0.079
1743932_1 -1.605 0.329 1 1 14 1055 518 116 62 3671 1649 160 118 0 -1.605
1745264_1 1.021 2.029 1 1 15 3762 803 136 86 2401 1392 204 179 0 1.021
1746524_1 1.040 1 1 16 282 234 150 105 470 244 314 269 -50 0.057
1747856_1 0.762 1 1 17 288 137 200 160 697 301 555 511 -50 -0.392
1749116_1 0.307 1 1 18 353 150 268 169 1271 579 931 546 -50 -1.702
1750448_1 0.540 1.454 1 1 19 6240 2329 229 449 5785 2641 701 444 0 0.540
1751708_1 0.851 1.804 1 1 20 16587 1163 190 149 11654 1441 477 290 0 0.851

Total number of rows: 35024

Table truncated, full table size 2438 Kbytes.




Supplementary file Size Download File type/resource
GSM343496.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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