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Sample GSM110526 Query DataSets for GSM110526
Status Public on Oct 17, 2006
Title siFBP1_Set A - 1st array - mAdbID:73261
Sample type RNA
 
Channel 1
Source name Set A_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 A_siFBP1
Organism Homo sapiens
Characteristics Cell type: primary skin fibroblast (Hs68)
Treatment protocol Treatment type: compound
Agent: Stealth siRNA targeting FBP1
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: 73261
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 0.464 1.379 1 1 1 27155 6890 143 147 18319 7338 234 774 0 0.464
1728380_1 0.144 1.105 1 1 2 64846 1709 100 250 54349 7766 250 124 0 0.144
1729712_1 -0.044 0.970 1 1 3 7581 2169 106 209 7337 2121 221 105 0 -0.044
1730972_1 -0.148 0.903 1 1 4 837 404 97 121 990 490 233 111 0 -0.148
1732304_1 -0.769 0.587 1 1 5 457 323 108 111 748 402 199 116 0 -0.769
1733564_1 -0.519 0.698 1 1 6 11042 2211 156 166 14620 1737 221 91 0 -0.519
1734896_1 0.313 1 1 7 151 124 111 142 339 238 221 112 -50 -1.676
1736156_1 0.941 1.920 1 1 8 12307 10593 118 126 6089 5081 227 100 0 0.941
1737488_1 0.476 1.391 1 1 9 9742 2934 115 136 6619 1773 229 94 0 0.476
1738748_1 -1.106 0.465 1 1 10 367 292 124 102 699 290 216 111 0 -1.106
1740080_1 0.610 1.527 1 1 11 3942 1927 124 111 2558 1362 249 120 0 0.610
1741340_1 -0.374 0.772 1 1 12 1245 883 114 211 1603 672 250 110 0 -0.374
1742672_1 -1.708 0.306 1 1 13 515 326 112 116 1434 1021 218 106 0 -1.708
1743932_1 0.434 1.351 1 1 14 17387 6438 113 131 12014 5087 211 649 0 0.434
1745264_1 0.181 1.133 1 1 15 24533 6879 112 87 20135 2760 240 106 0 0.181
1746524_1 -0.100 0.933 1 1 16 1673 673 92 96 1780 1137 215 93 0 -0.100
1747856_1 1.075 1 1 17 176 231 105 125 276 171 215 107 -50 0.104
1749116_1 -1.024 0.492 1 1 18 1328 977 115 136 2482 709 205 112 0 -1.024
1750448_1 -0.171 0.888 1 1 19 61900 7848 134 136 64393 3955 192 113 0 -0.171
1751708_1 -1.618 0.326 1 1 20 3257 998 129 143 9078 2926 215 100 0 -1.618

Total number of rows: 35024

Table truncated, full table size 2455 Kbytes.




Supplementary file Size Download File type/resource
GSM110526.gpr.gz 4.0 Mb (ftp)(http) GPR
Raw data provided as supplementary file

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