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Sample GSM110530 Query DataSets for GSM110530
Status Public on Oct 17, 2006
Title siFBP2_Set B - 2nd array - mAdbID:74112
Sample type RNA
 
Channel 1
Source name Set B_control siRNA
Organism Homo sapiens
Characteristics Cell type: primary skin fibroblast (Hs68)
Treatment protocol Treatment type: compound
Agent: Stealth negative control siRNA
Treatment dose: 50 nM
Treatment time: 2 days
Extracted molecule total RNA
Extraction protocol Sample Extraction Protocol
Extraction method: Trizol
Label cy3
Label protocol Cy3 Sample Labeling Protocol - generic
 
Channel 2
Source name Set B_siFBP2
Organism Homo sapiens
Characteristics Cell type: primary skin fibroblast (Hs68)
Treatment protocol Treatment type: compound
Agent: Stealth siRNA targeting FBP2
Treatment dose: 50 nM
Treatment time: 2 days
Extracted molecule total RNA
Extraction protocol Sample Extraction Protocol
Extraction method: Trizol
Label cy5
Label protocol Cy5 Sample Labeling Protocol - generic
 
 
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 42øC 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 100øC 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 42øC 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 42øC 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")
Description mAdb experiment ID: 74112
Data processing 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 May 24, 2006
Last update date Oct 17, 2006
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)
GSE4914 RNAi analysis of the FBP transactivator family

Data table header descriptions
ID_REF NCI mAdb well id plus replicate number
VALUE same as UNF_VALUE but with flagged values removed
Ratio 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 ratio

Data table
ID_REF VALUE Ratio 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 0.661 1.581 1 1 1 2650 630 98 71 2623 522 223 91 0 0.661
1728380_1 0.228 1.171 1 1 2 20172 6159 110 144 25704 6828 236 294 0 0.228
1729712_1 0.273 1.209 1 1 3 1200 428 102 85 1605 493 254 149 0 0.273
1730972_1 1.133 2.193 1 1 4 236 125 121 89 372 136 294 154 0 1.133
1732304_1 0.455 1 1 5 132 100 106 69 359 125 274 118 -50 -1.136
1733564_1 -0.618 0.651 1 1 6 1460 585 102 71 3384 1199 284 119 0 -0.618
1734896_1 1.487 1 1 7 103 62 103 62 287 114 303 117 -50 0.573
1736156_1 0.404 1.323 1 1 8 3633 2116 102 61 4289 1354 320 125 0 0.404
1737488_1 -0.115 0.923 1 1 9 1415 569 98 49 2441 697 320 227 0 -0.115
1738748_1 -1.138 0.455 1 1 10 211 184 97 65 686 268 313 188 0 -1.138
1740080_1 -0.255 0.838 1 1 11 873 568 101 92 1669 586 299 122 0 -0.255
1741340_1 0.270 1 1 12 128 81 102 74 439 169 296 152 -50 -1.887
1742672_1 0.307 1.237 1 1 13 166 150 77 59 440 195 333 278 0 0.307
1743932_1 -0.091 0.939 1 1 14 3125 1212 101 66 5088 1736 299 146 0 -0.091
1745264_1 0.497 1.411 1 1 15 11529 3910 95 53 12335 3627 288 147 0 0.497
1746524_1 0.328 1.255 1 1 16 316 183 94 48 551 200 288 157 0 0.328
1747856_1 -1.153 0.450 1 1 17 132 74 93 59 417 387 288 129 0 -1.153
1749116_1 -0.014 0.990 1 1 18 346 176 89 72 653 187 267 187 0 -0.014
1750448_1 -0.358 0.780 1 1 19 7252 4111 89 73 13916 7949 259 166 0 -0.358
1751708_1 -0.302 0.811 1 1 20 2021 612 84 64 3803 880 252 125 0 -0.302

Total number of rows: 35024

Table truncated, full table size 2356 Kbytes.




Supplementary file Size Download File type/resource
GSM110530.gpr.gz 3.9 Mb (ftp)(http) GPR
Raw data provided as supplementary file

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