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Sample GSM152046 Query DataSets for GSM152046
Status Public on Apr 01, 2007
Title C6042
Sample type RNA
 
Channel 1
Source name C6042 tumor biopsy
Organism Homo sapiens
Characteristics ERalpha Positive;ERbeta Positive
Biomaterial provider Dept. of Oncology, Lund University, Sweden
Treatment protocol n/a
Growth protocol n/a
Extracted molecule total RNA
Extraction protocol Tissue homogenization and RNA recovery using TRIzol reagent (Invitrogen), followed by 2nd round of purification using RNeasy kit (Qiagen).
Label Cy3
Label protocol 25 ug total RNA; anchored oligo-dT primers and CyScribe indirect amino-allyl cDNA synthesis and labeling protocol, with purification using GFX columns (all from Amersham Biosciences).
 
Channel 2
Source name Stratagene Universal Human Reference
Organism Homo sapiens
Characteristics See Stratagene product # 740000.
Biomaterial provider Stratagene
Treatment protocol See Stratagene product # 740000.
Growth protocol See Stratagene product # 740000.
Extracted molecule total RNA
Extraction protocol See Stratagene product # 740000.
Label Cy5
Label protocol 15 ug total RNA; anchored oligo-dT primers and CyScribe indirect amino-allyl cDNA synthesis and labeling protocol, with purification using GFX columns (all from Amersham Biosciences).
 
 
Hybridization protocol Labeled targets were pooled and combined with blocking agents (12 ug poly-dA, 6 ug yeast tRNA, 20 ug Cot-1 DNA), and hybridized to microarray using the Pronto Universal Hybridization System (Corning) for 18 hours in a humidified chamber (Corning) submerged in a 42 C water bath. Slide was washing using the Pronto Universal Hybridization System.
Scan protocol Scanned using the Agilent DNA Microarray Scanner at 10 micron resolution. The TIFF image was split and analyzed with GenePix 4.1.1.4. Result files were loaded into BioArray Software Environment. Cy3=channel 1, Cy5=channel 2.
Description Human breast tumor sample
Data processing Data was preprocessed in the BioArray Software Environment. For each channel, the Median FG - Median BG intensity value was used. Features flagged bad/missing during image analysis were removed. Data was normalized using pin-based LOWESS (6 groups of 8 pins/group). Filtering on median Signal-to-Noise ratio was applied, keeping only those datapoints with a ch1median or ch2median SNR>=3. Features that were present in at least 80% of the 88 tumors in the series were kept, all other features were removed. Features with a variation <0.45 SD of log2(ratio) were removed. Genes and arrays were then median centered 1X.
 
Submission date Dec 20, 2006
Last update date Feb 26, 2007
Contact name Sofia K Gruvberger-Saal
E-mail(s) sg2414@columbia.edu
Phone 212-851-5263
Organization name Columbia University
Department Institute for Cancer Genetics
Street address 1130 St. Nicholas Ave., ICRC 406
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platform ID GPL3883
Series (1)
GSE6577 Estrogen receptor beta expression is associated with tamoxifen response in ER alpha-negative breast carcinoma

Data table header descriptions
ID_REF unique position on array platform
VALUE log2 ratio (tumor ch1=532nm/reference ch2=635nm) after filtering and normalization procedures.

Data table
ID_REF VALUE
6 -0.252247728
13 -0.333027841
15 0.596521574
16 0.898021952
17 0.386142267
20 0.11053483
26 -0.067301275
31 0.461070315
32 1.06490719
34 0.70115103
44 -0.387077845
47 0.029448701
50 -1.270006985
53 -1.031702246
54 1.020733536
56 -0.065543278
57 0.235046115
58 -0.058013467
59 -2.353838881
61 0.02263711

Total number of rows: 11171

Table truncated, full table size 195 Kbytes.




Supplementary file Size Download File type/resource
GSM152046.gpr.gz 2.4 Mb (ftp)(http) GPR

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