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Sample GSM135614 Query DataSets for GSM135614
Status Public on Mar 14, 2009
Title Human_TK4T_clinically isolated tissue
Sample type RNA
 
Source name human breast cancer
Organism Homo sapiens
Characteristics clinical isolate, flash-frozen
Treatment protocol Tissues were surgically isolated and were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was extracted using the Sepasol-I (WAKO)
Growth protocol not received any pre-operative adjuvant hormone or chemotherapy
Extracted molecule total RNA
Extraction protocol Qiagen RNeasy kit
Label biotin
Label protocol Enzo Biotin labeling
 
Hybridization protocol According to standard Affymetrix protocol. 15ug of cRNA was fragmented, fragmented product was checked on gel(average size 100nt), Hybridization cocktail added and hybed on HG_U133A arrays. Washed with non-stringent wash buffer (A) and stained with SAPE solution.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
 
Submission date Sep 11, 2006
Last update date Mar 16, 2009
Contact name shinobu Masuda
E-mail(s) masuda.shinobu@nihon-u.ac.jp
Phone 81-3-3972-8111
Organization name Nihon Univeristy School of Medicine
Department pathology
Street address 30-1 Ohyaguchikami-cho
City Itabashi
State/province Tokyo
ZIP/Postal code 173-8610
Country Japan
 
Platform ID GPL8300
Series (1)
GSE6367 Gene profile of breast cancers with immunohistochemical phenotypes of ER+/- and/or HER2+/-

Data table header descriptions
ID_REF
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
100_g_at 270.6 A 0.204022
1000_at 598.7 P 0.00418
1001_at 84.5 A 0.107301
1002_f_at 37 A 0.339558
1003_s_at 148 A 0.339558
1004_at 143.4 A 0.234557
1005_at 1239.2 P 0.000219
1006_at 3.2 A 0.824011
1007_s_at 1873 P 0.000322
1008_f_at 1472 P 0.000219
1009_at 2655 P 0.000266
101_at 155 A 0.089405
1010_at 20.5 A 0.732537
1011_s_at 1154.2 P 0.000219
1012_at 16.3 A 0.339558
1013_at 132.7 P 0.000322
1014_at 416 A 0.07383
1015_s_at 39.5 A 0.715253
1016_s_at 43.6 A 0.378184
1017_at 80.5 P 0.021866

Total number of rows: 12623

Table truncated, full table size 314 Kbytes.




Supplementary file Size Download File type/resource
GSM135614.CEL.gz 2.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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