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Sample GSM135629 Query DataSets for GSM135629
Status Public on Mar 14, 2009
Title Human_TK18T_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 347.3 A 0.127645
1000_at 682 P 0.005643
1001_at 70.6 A 0.07383
1002_f_at 16.4 A 0.64131
1003_s_at 57.1 A 0.64131
1004_at 103.1 A 0.218983
1005_at 731.3 P 0.002228
1006_at 1.9 A 0.88284
1007_s_at 1395.4 P 0.000468
1008_f_at 3239.5 P 0.000388
1009_at 2097.2 P 0.000266
101_at 23.4 A 0.660442
1010_at 28.6 A 0.52062
1011_s_at 448.1 P 0.000388
1012_at 21.2 A 0.302547
1013_at 241.9 P 0.000219
1014_at 368.6 A 0.081337
1015_s_at 36.7 A 0.561639
1016_s_at 33.3 A 0.107301
1017_at 93.4 P 0.007543

Total number of rows: 12623

Table truncated, full table size 313 Kbytes.

Supplementary file Size Download File type/resource
GSM135629.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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