|
| Status |
Public on Oct 17, 2006 |
| Title |
MCF7_Self-Self_ExpressionProfile_HO87-H6 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
MCF7
|
| Organism |
Homo sapiens |
| Characteristics |
MCF7 human breast carcinoma cells
|
| Biomaterial provider |
MCF7 cell line used within the Netherlands Cancer Institute
|
| Growth protocol |
MCF7 cells were maintained in DMEM medium supplemented with 10% FCS and antibiotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Detailed protocols for RNA isolation, amplification, labeling, and hybridization can be found at http://microarrays.nki.nl/download/protocols.html.
|
| Label |
Cy5
|
| Label protocol |
Detailed protocols for RNA isolation, amplification, labeling, and hybridization can be found at http://microarrays.nki.nl/download/protocols.html.
|
| |
|
| Channel 2 |
| Source name |
MCF7
|
| Organism |
Homo sapiens |
| Characteristics |
MCF7 human breast carcinoma cells
|
| Biomaterial provider |
MCF7 cell line used within the Netherlands Cancer Institute
|
| Growth protocol |
MCF7 cells were maintained in DMEM medium supplemented with 10% FCS and antibiotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Detailed protocols for RNA isolation, amplification, labeling, and hybridization can be found at http://microarrays.nki.nl/download/protocols.html.
|
| Label |
Cy3
|
| Label protocol |
Detailed protocols for RNA isolation, amplification, labeling, and hybridization can be found at http://microarrays.nki.nl/download/protocols.html.
|
| |
|
| |
| Hybridization protocol |
Detailed protocols for RNA isolation, amplification, labeling, and hybridization can be found at http://microarrays.nki.nl/download/protocols.html.
|
| Scan protocol |
Arrays were scanned using a Agilent Technologies Scanner, Model: G2505B and ChipScan software.
Image analyses were done using Imagene 6.0 software (BioDiscvovery)
|
| Description |
Self-Self Expression profile. Both channels contain amplified RNA isolated from MCF7 cells.
|
| Data processing |
Data was background corrected and normalized using a LOWESS fit per subarray, Column VALUE contains the normalized log2 expression ratios for each individual array.
|
| |
|
| Submission date |
Aug 03, 2006 |
| Last update date |
Oct 17, 2006 |
| Contact name |
Bas van Steensel |
| E-mail(s) |
b.v.steensel@nki.nl
|
| Phone |
+ 31 20 512 2040
|
| Fax |
+31 20 669 1383
|
| URL |
http://www.nki.nl/nkidep/vansteensel
|
| Organization name |
Netherlands Cancer Institute
|
| Department |
division of Molecular Biology
|
| Lab |
van Steensel group
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| ZIP/Postal code |
1066 CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL3676 |
| Series (1) |
| GSE5445 |
Human Heterochromatin Proteins form Large Domains Containing KRAB-ZNF Genes |
|
| Data table header descriptions |
| ID_REF |
|
| Red Signal Mean |
pixel intensity averaged over the local signal region (ImaGene) |
| Red Background Mean |
pixel intensity averaged over the local background region (ImaGene) |
| Red Signal Median |
median pixel intensity computed over the local signal region (ImaGene) |
| Red Background Median |
median pixel intensity computed over the local background region (ImaGene) |
| Red Signal Stdev |
standard deviation of pixel intensities over the local signal region (ImaGene) |
| Red Background Stdev |
standard deviation of pixel intensities over the local background region (ImaGene) |
| Green Signal Mean |
pixel intensity averaged over the local signal region (ImaGene) |
| Green Background Mean |
pixel intensity averaged over the local background region (ImaGene) |
| Green Signal Median |
median pixel intensity computed over the local signal region (ImaGene) |
| Green Background Median |
median pixel intensity computed over the local background region (ImaGene) |
| Green Signal Stdev |
standard deviation of pixel intensities over the local signal region (ImaGene) |
| Green Background Stdev |
standard deviation of pixel intensities over the local background region (ImaGene) |
| VALUE |
Normalized log2 ratio |
| A |
Normalized fluorescence spot intensity (log2 ?Cy5*Cy3) |
