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Sample GSM135621 Query DataSets for GSM135621
Status Public on Mar 14, 2009
Title Human_TK10T_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
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
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
100_g_at 380.6 A 0.218983
1000_at 542.9 P 0.017001
1001_at 137.3 P 0.019304
1002_f_at 18.2 A 0.561639
1003_s_at 172.7 A 0.47938
1004_at 63.3 A 0.339558
1005_at 1209.8 P 0.000468
1006_at 144.2 P 0.009985
1007_s_at 1715.1 P 0.000468
1008_f_at 1826.9 P 0.000805
1009_at 1398.2 P 0.000266
101_at 95.9 A 0.35869
1010_at 12.8 A 0.837065
1011_s_at 389.7 P 0.000219
1012_at 29.1 A 0.438361
1013_at 118.7 P 0.000322
1014_at 400 A 0.107301
1015_s_at 71.4 A 0.5
1016_s_at 27.4 A 0.47938
1017_at 98.1 P 0.013092

Total number of rows: 12623

Table truncated, full table size 314 Kbytes.

Supplementary file Size Download File type/resource
GSM135621.CEL.gz 2.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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