NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM135628 Query DataSets for GSM135628
Status Public on Mar 14, 2009
Title Human_TK17T_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 369.5 A 0.162935
1000_at 769.2 P 0.011447
1001_at 157.3 A 0.07383
1002_f_at 24.4 A 0.5
1003_s_at 192.4 A 0.438361
1004_at 234.4 A 0.339558
1005_at 663 P 0.002617
1006_at 10.4 A 0.697453
1007_s_at 2377.2 P 0.001141
1008_f_at 2574.6 P 0.000805
1009_at 2382.1 P 0.000266
101_at 173.3 A 0.175989
1010_at 7.2 A 0.892699
1011_s_at 280.3 P 0.003067
1012_at 10.2 A 0.64131
1013_at 52.2 A 0.138765
1014_at 524.3 A 0.11716
1015_s_at 16 A 0.951005
1016_s_at 44.4 A 0.339558
1017_at 63.6 P 0.019304

Total number of rows: 12623

Table truncated, full table size 313 Kbytes.




Supplementary file Size Download File type/resource
GSM135628.CEL.gz 2.9 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap