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Sample GSM343494 Query DataSets for GSM343494
Status Public on May 18, 2011
Title GFP-JTV Transfection - repeat 1 - mAdbID:75970
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: 1.92;; 2.72
Temperature: 34.84
Description mAdb experiment ID: 75970
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 0.637 1.555 1 1 1 6682 1532 70 68 6019 932 151 97 0 0.637
1728380_1 0.533 1.447 1 1 2 4906 553 69 53 4769 776 157 94 0 0.533
1729712_1 0.515 1.429 1 1 3 2214 592 69 69 2236 621 165 134 0 0.515
1730972_1 0.590 1.505 1 1 4 220 168 64 48 317 115 174 106 0 0.590
1732304_1 0.199 1.148 1 1 5 297 215 69 65 436 148 162 116 0 0.199
1733564_1 1.758 3.382 1 1 6 261 255 60 85 298 57 216 112 0 1.758
1734896_1 -0.924 0.527 1 1 7 129 106 74 65 323 81 179 122 0 -0.924
1736156_1 0.557 1.471 1 1 8 2373 533 79 85 2330 601 178 97 0 0.557
1737488_1 0.495 1.409 1 1 9 2202 593 78 83 2255 436 175 89 0 0.495
1738748_1 0.637 1.556 1 1 10 309 285 79 79 394 110 190 95 0 0.637
1740080_1 0.609 1.525 1 1 11 585 338 71 83 655 179 190 112 0 0.609
1741340_1 0.142 1.104 1 1 12 183 95 71 92 340 123 200 126 0 0.142
1742672_1 0.495 1.409 1 1 13 462 199 82 76 567 311 195 123 0 0.495
1743932_1 0.482 1.397 1 1 14 3763 1149 82 77 3835 988 199 109 0 0.482
1745264_1 1.023 2.032 1 1 15 1337 770 78 78 1060 346 205 102 0 1.023
1746524_1 0.529 1.442 1 1 16 543 335 83 84 645 170 205 116 0 0.529
1747856_1 0.255 1.193 1 1 17 310 354 86 131 473 178 214 110 0 0.255
1749116_1 0.274 1.209 1 1 18 394 186 82 80 577 132 221 140 0 0.274
1750448_1 0.422 1.340 1 1 19 14315 5648 93 82 14875 2053 230 117 0 0.422
1751708_1 0.582 1.497 1 1 20 4081 695 87 90 3897 682 216 123 0 0.582

Total number of rows: 35024

Table truncated, full table size 2384 Kbytes.




Supplementary file Size Download File type/resource
GSM343494.gpr.gz 3.9 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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