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Sample GSM110531 Query DataSets for GSM110531
Status Public on Oct 17, 2006
Title siFBP3_Set B - 2nd array - mAdbID:74113
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_siFBP3
Organism Homo sapiens
Characteristics Cell type: primary skin fibroblast (Hs68)
Treatment protocol Treatment type: compound
Agent: Stealth siRNA targeting FBP3
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: 74113
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 0.566 1.480 1 1 1 1981 776 162 155 1962 441 303 128 0 0.566
1728380_1 0.358 1.282 1 1 2 14985 5117 175 124 15927 4819 332 172 0 0.358
1729712_1 0.111 1.080 1 1 3 723 462 150 131 1053 459 337 147 0 0.111
1730972_1 1.507 1 1 4 277 181 181 130 442 187 356 272 -50 0.591
1732304_1 0.015 1 1 5 172 143 188 161 458 230 369 172 -50 -6.043
1733564_1 -0.528 0.693 1 1 6 1518 776 211 201 2924 912 380 199 0 -0.528
1734896_1 1.800 1 1 7 246 162 194 158 450 173 411 197 -50 0.848
1736156_1 0.663 1.583 1 1 8 3526 1124 202 133 3245 823 411 180 0 0.663
1737488_1 0.172 1.127 1 1 9 1303 554 181 232 1800 537 456 201 0 0.172
1738748_1 1.178 1 1 10 249 145 194 182 484 199 421 172 -50 0.237
1740080_1 0.666 1.587 1 1 11 914 588 211 167 1045 464 447 165 0 0.666
1741340_1 -0.034 0.977 1 1 12 355 271 224 172 650 265 469 212 0 -0.034
1742672_1 0.715 1 1 13 234 187 216 186 473 196 439 389 -50 -0.485
1743932_1 0.458 1.374 1 1 14 4011 1343 193 145 4197 1211 446 160 0 0.458
1745264_1 0.200 1.148 1 1 15 7863 6187 196 185 9426 7604 415 184 0 0.200
1746524_1 0.763 1 1 16 357 327 206 246 695 720 428 644 -50 -0.390
1747856_1 0.041 1 1 17 248 177 256 406 502 200 469 922 -50 -4.612
1749116_1 0.927 1 1 18 437 219 235 419 790 661 496 867 -100 -0.109
1750448_1 -0.028 0.981 1 1 19 9923 5707 236 313 13796 7918 466 413 0 -0.028
1751708_1 0.039 1.028 1 1 20 2232 617 196 175 3175 740 501 213 0 0.039

Total number of rows: 35024

Table truncated, full table size 2392 Kbytes.




Supplementary file Size Download File type/resource
GSM110531.gpr.gz 3.9 Mb (ftp)(http) GPR
Raw data provided as supplementary file

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