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Sample GSM508736 Query DataSets for GSM508736
Status Public on Mar 18, 2011
Title N302595
Sample type RNA
 
Channel 1
Source name Human Reference B
Organism Homo sapiens
Characteristics reference: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs
Biomaterial provider Stratagene
Extracted molecule total RNA
Extraction protocol Total RNA isolated by stratagene
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
Channel 2
Source name N302595
Organism Homo sapiens
Characteristics slidename: H1AUNC44K-H1-0505
sample: N302595
study: Xena
intrinsic subtypes by pam50: LumA
p53 status by amplichip: WILDTYPE
p53 measured by ihc: POSITIVE
tumor size (cm): 7
grade: 1
er (0 = negative; 1 = positive): 1
pgr (0 = negative; 1 = positive): 1
her2 (0 = negative; 1 = positive): 0
response: PARTIAL RESPONSE
neoadjuvant chemotherapy: docetaxel-Capecitabine
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-124
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 5.1 analysis software.
Description N302595
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Feb 11, 2010
Last update date Jun 06, 2022
Contact name Charles M. Perou
E-mail(s) cperou@med.unc.edu
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 GPL5325
Series (1)
GSE22358 Clinical and Pathologic Response of the Primary Tumor in Women Receiving Neoadjuvant Docetaxel-Capecitabine (+/- Trastuzumab) Chemotherapy
Relations
Reanalyzed by GSE205568

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
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 channel 2 normalized over channel 1 (global normalization)
CORR correlation coefficient among pixels
FLAG Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots
UNF_VALUE log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_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 UNF_VALUE
1 .07 1 63 10 37 6 86 33 56 23 303 52 49 76 27 28 .054 .38 0 .07
2 .341 2 64 9 36 6 91 34 52 23 283 52 46 80 29 37 .28 .51 0 .341
3 .656 3 41 8 35 6 63 22 54 23 364 80 47 55 5 9 .415 .17 0 .656
4 -.961 4 82 12 36 8 83 29 57 22 286 52 50 73 48 24 -1 .31 0 -.961
5 .108 5 182 39 36 6 227 85 56 23 357 80 49 200 152 164 .048 .83 0 .108
6 .379 6 2631 456 38 17 3605 942 58 57 374 80 51 3190 2659 3458 .276 .96 0 .379
7 .16 7 1291 248 38 8 1528 395 60 210 370 80 53 1352 1282 1433 .052 .95 0 .16
8 .16 8 360 61 37 7 446 119 57 27 369 80 50 394 335 374 .091 .93 0 .16
9 1.91 9 14345 3524 36 13 60400 14767 68 1691 358 80 60 53451 15157 56955 1.9 .9 0 1.91
10 -.339 10 2314 514 39 27 1949 626 62 1712 349 80 54 1724 2330 1842 -.446 .96 0 -.339
11 .15 11 1024 215 37 6 1209 390 59 22 347 80 52 1069 1011 1122 .043 .96 0 .15
12 -.137 12 67 12 37 6 91 35 61 25 244 52 53 80 31 28 -.152 .33 0 -.137
13 .42 13 43 7 38 6 66 25 60 25 376 80 53 58 4 6 0 .04 0 .42
14 .64 14 2721 306 38 14 4467 675 65 57 311 52 57 3953 2752 4290 .538 .97 0 .64
15 .449 15 3200 960 38 12 4613 1056 64 53 341 80 56 4082 3246 4430 .348 .96 0 .449
16 -.413 16 2562 712 38 6 2050 531 61 23 337 80 53 1814 2585 1941 -.519 .95 0 -.413
17 -.416 17 288 76 38 6 264 83 61 25 368 80 53 233 260 195 -.474 .87 0 -.416
18 .726 18 143 28 38 43 252 76 63 154 369 80 55 223 109 181 .678 .82 0 .726
19 -2.445 19 996 226 38 6 251 66 62 26 359 80 54 222 992 182 -2.515 .88 0 -2.445
20 .139 20 70 9 37 6 102 35 62 25 299 52 54 90 34 38 .126 .4 0 .139

Total number of rows: 44290

Table truncated, full table size 3524 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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