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Sample GSM110529 Query DataSets for GSM110529
Status Public on Oct 17, 2006
Title siFBP1_Set B - 2nd array - mAdbID:74111
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_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: 74111
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 0.187 1.139 1 1 1 3033 1467 207 133 3024 1258 428 179 0 0.187
1728380_1 -0.184 0.880 1 1 2 24941 13587 221 150 29813 11004 444 151 0 -0.184
1729712_1 -0.021 0.985 1 1 3 1520 569 236 126 1797 908 434 158 0 -0.021
1730972_1 1.268 1 1 4 315 227 212 133 521 190 436 208 -50 0.342
1732304_1 0.470 1 1 5 236 137 192 127 505 179 407 167 -50 -1.090
1733564_1 -0.108 0.928 1 1 6 3324 654 229 150 3877 1116 387 147 0 -0.108
1734896_1 1.511 1 1 7 246 166 220 157 424 177 406 143 -50 0.595
1736156_1 0.486 1.400 1 1 8 9272 1688 215 159 7174 1066 408 151 0 0.486
1737488_1 0.163 1.120 1 1 9 4591 1347 207 161 4507 1365 412 171 0 0.163
1738748_1 0.497 1 1 10 300 186 214 157 598 261 417 168 -50 -1.009
1740080_1 -0.032 0.978 1 1 11 1946 448 214 170 2279 609 427 151 0 -0.032
1741340_1 -1.341 0.395 1 1 12 396 197 213 146 911 313 426 155 0 -1.341
1742672_1 0.537 1 1 13 262 142 203 127 527 218 412 151 -50 -0.898
1743932_1 0.498 1.413 1 1 14 8093 4372 209 144 6273 3293 435 162 0 0.498
1745264_1 -0.060 0.959 1 1 15 13749 5246 222 118 15185 4552 430 141 0 -0.060
1746524_1 -1.215 0.431 1 1 16 339 178 234 167 647 156 392 147 0 -1.215
1747856_1 -0.198 0.872 1 1 17 401 158 231 175 653 175 449 215 0 -0.198
1749116_1 0.262 1.199 1 1 18 513 174 216 124 697 163 438 169 0 0.262
1750448_1 0.052 1.036 1 1 19 14094 3558 199 136 14439 3449 415 139 0 0.052
1751708_1 -0.471 0.721 1 1 20 2590 993 217 135 3860 1508 419 165 0 -0.471

Total number of rows: 35024

Table truncated, full table size 2404 Kbytes.




Supplementary file Size Download File type/resource
GSM110529.gpr.gz 4.0 Mb (ftp)(http) GPR
Raw data provided as supplementary file

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