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Sample GSM110528 Query DataSets for GSM110528
Status Public on Oct 17, 2006
Title siFBP2_Set A - 1st array - mAdbID:73427
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_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: 73427
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 0.593 1.509 1 1 1 844 720 54 29 702 657 61 44 0 0.593
1728380_1 -0.165 0.892 1 1 2 4591 4569 51 29 6298 6060 68 53 0 -0.165
1729712_1 0.378 1.300 1 1 3 659 588 56 81 638 634 70 93 0 0.378
1730972_1 0.083 1.059 1 1 4 130 84 53 33 150 60 61 30 0 0.083
1732304_1 0.126 1.091 1 1 5 91 26 50 20 107 33 61 21 0 0.126
1733564_1 -0.108 0.928 1 1 6 917 775 50 26 1209 1099 65 40 0 -0.108
1734896_1 1.224 1 1 7 60 37 61 138 80 44 84 334 -50 0.292
1736156_1 0.607 1.523 1 1 8 3206 686 105 211 2672 338 179 516 0 0.607
1737488_1 0.720 1 1 9 707 721 287 236 1490 775 776 616 -50 -0.474
1738748_1 0.423 1 1 10 231 174 192 266 655 597 542 726 -50 -1.243
1740080_1 -0.478 0.718 1 1 11 665 627 50 24 1113 449 64 25 0 -0.478
1741340_1 -0.182 0.881 1 1 12 160 143 52 26 226 108 76 47 0 -0.182
1742672_1 -0.870 0.547 1 1 13 84 35 42 28 159 76 65 30 0 -0.870
1743932_1 0.176 1.130 1 1 14 9720 1934 62 29 10537 1658 74 57 0 0.176
1745264_1 -0.030 0.979 1 1 15 4718 2398 55 32 5902 4146 73 45 0 -0.030
1746524_1 0.929 1.904 1 1 16 220 116 52 35 187 97 79 51 0 0.929
1747856_1 0.322 1 1 17 60 33 55 46 95 38 76 62 -50 -1.634
1749116_1 -0.442 0.736 1 1 18 140 84 54 33 216 126 73 43 0 -0.442
1750448_1 0.179 1.132 1 1 19 23650 12374 52 49 25605 17255 79 33 0 0.179
1751708_1 0.134 1.097 1 1 20 1787 311 52 36 2017 416 81 41 0 0.134

Total number of rows: 35024

Table truncated, full table size 2312 Kbytes.




Supplementary file Size Download File type/resource
GSM110528.gpr.gz 4.0 Mb (ftp)(http) GPR
Raw data provided as supplementary file

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