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Sample GSM71551 Query DataSets for GSM71551
Status Public on Feb 20, 2007
Title ME16C+p53RNAi, 24h Sham
Sample type RNA
 
Channel 1
Source name ME16C pool
Organism Homo sapiens
Characteristics Cell Line messenger RNA
Biomaterial provider Melissa Troester UNC-CH
Extracted molecule polyA RNA
Extraction protocol Harvest cells by scraping, use invitrogen Micro-FastTrack to extract mRNA
Label Cy3
Label protocol Agilent direct labeling kit
 
Channel 2
Source name ME16C+p53RNAi, 24h Sham
Organism Homo sapiens
Characteristics Cell Line messenger RNA
Biomaterial provider Melissa Troester UNC-CH
Growth protocol Cells grown for to 60-80% confluence in MEGM media (Clonetics), harvested 48 hours after feeding, 4 harvests were pooled
Extracted molecule polyA RNA
Extraction protocol Harvest cells by scraping, use invitrogen Micro-FastTrack to extract mRNA
Label Cy5
Label protocol Agilent direct labeling kit
 
 
Hybridization protocol Agilent direct labeling kit
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.1 analysis software
Description ME16C+p53RNAi, 24h Sham
Data processing Data was filtered for Lowess normalized net (mean) >30 in both channels and flagged values removed, only genes with 70% good data were used, log base 2 expression ratios given in the data table.
 
Submission date Aug 23, 2005
Last update date Jul 17, 2015
Contact name Charles M. Perou
E-mail(s) [email protected]
Organization name University of North Carolina at Chapel Hill
Department Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center
Street address 12-044 Lineberger Comprehensive Cancer Center CB# 7295
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7264
Country USA
 
Platform ID GPL885
Series (1)
GSE3178 Gene expression patterns associated with p53 status in breast cancer

Data table header descriptions
ID_REF Spot Reference ID
VALUE same as UNF_VALUE but with flagged values removed
SPOT spot number on array
CH1_MEAN channel 1 mean intensity
CH1_SD standard deviation of channel 1 intensity
CH1_BKD_MEDIAN channel 1 background median intensity
CH1_BKD_SD standard deviation of channel 1 background median intensity
CH2_MEAN channel 2 mean intensity
CH2_SD standard deviation of channel 2 intensity
CH2_BKD_MEDIAN channel 2 background median intensity
CH2_BKD_SD standard deviation of channel 2 background median intensity
TOT_BPIX number of background pixels
TOT_SPIX number of spot pixels
CH2BN_MEDIAN channel 2 normalized background median intensity
CH2IN_MEAN channel 2 normalized mean intensity
CH1DL_MEAN channel 1 Lowess_normalized mean intensity
CH2DL_MEAN channel 2 Lowess_normalized mean intensity
LOG_RAT2N_MEAN log2_ratio of (CH2IN_MEAN - CH2BN_MEDIAN) over (CH1_MEAN - CH1_BKD_MEDIAN), CH2IN_MEAN and CH2BN_MEDIAN are global-normalized intensities
CORR correlation coefficient among pixels
FLAG Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots
CONTROL Y: control gene; N: not control
UNF_VALUE LOG_RAT2L_MEAN; log2_ratio of CH2DL_MEAN over CH1DL_MEAN

Data table
ID_REF VALUE SPOT CH1_MEAN CH1_SD CH1_BKD_MEDIAN CH1_BKD_SD CH2_MEAN CH2_SD CH2_BKD_MEDIAN CH2_BKD_SD TOT_BPIX TOT_SPIX CH2BN_MEDIAN CH2IN_MEAN CH1DL_MEAN CH2DL_MEAN LOG_RAT2N_MEAN CORR FLAG CONTROL UNF_VALUE
1 -3.572 22575 856 315 70 63 124 72 85 59 552 156 96 140 603 50 -4.158 .2 0 Y -3.572
2 .205 22470 156 35 70 179 101 61 86 66 492 80 97 114 33 38 -2.336 .03 0 Y .205
3 -2.787 22365 156 40 71 158 92 60 86 65 630 120 97 104 59 8 -3.608 .13 0 N -2.787
4 .712 22260 10434 3787 71 41 27067 13419 85 64 647 156 96 30757 13063 21404 1.565 .98 0 N .712
5 .858 22155 557 219 70 64 943 485 79 75 636 156 89 1071 481 873 1.011 .92 0 N .858
6 .51 22050 72 15 68 61 98 58 83 66 488 120 94 111 6 9 2.087 .36 0 Y .51
7 -4.029 21945 891 342 69 65 109 66 82 66 568 156 93 123 601 36 -4.796 .12 0 Y -4.029
8 .533 21840 599 230 70 70 827 448 84 65 534 156 95 939 521 754 .674 .91 0 N .533
9 1.155 21735 243 82 71 51 335 182 88 64 619 156 100 380 138 307 .703 .71 0 N 1.155
10 -1.096 21630 81 27 71 36 90 60 81 66 520 120 92 102 13 6 0 .08 0 Y -1.096
11 .553 21525 278 95 72 216 279 162 88 68 594 156 100 317 163 240 .075 .53 0 N .553
12 0 21420 75 16 75 235 93 54 85 66 540 120 96 105 0 0 0 .19 0 Y 0
13 .693 21315 182 46 78 88 128 82 83 59 358 52 94 145 53 86 -1.029 .09 0 N .693
14 -3.765 21210 958 344 73 40 122 78 82 58 649 156 93 138 693 51 -4.293 .18 0 Y -3.765
15 .734 21105 1537 545 70 17 2997 1339 87 57 607 156 98 3405 1601 2665 1.172 .97 0 N .734
16 .746 21000 207 65 68 51 198 113 88 59 546 156 100 225 95 160 -.154 .56 0 N .746
17 .407 20895 179 25 68 82 116 71 81 66 506 120 92 131 54 71 -1.51 .11 0 N .407
18 .854 20790 79 50 70 135 100 67 81 92 584 120 92 113 9 17 1.222 .45 0 Y .854
19 -.279 20685 73 19 71 118 93 61 83 90 551 120 94 105 4 4 2.459 .44 0 Y -.279
20 1.584 20580 75 24 72 37 105 67 83 66 523 120 94 119 4 14 3.059 .16 0 Y 1.584

Total number of rows: 22575

Table truncated, full table size 1870 Kbytes.




Supplementary data files not provided
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