|
| Status |
Public on Dec 24, 2011 |
| Title |
BRCA1_1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Universal Human Reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample description: pool of total RNA from 10 human cell lines
|
| Growth protocol |
Cell lines were cultured in DMEM medium supplemented with 10%FBS, 0.08% Fungizone and 100units/mL penicillin/streptomycin, and maintained at 37ºC in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cell lines using Trizol (Invitrogen) according to the instructions of the manufacturer.
|
| Label |
Cy3
|
| Label protocol |
500 ng of total RNA from samples and Universal Human Reference RNA (Stratagene, Catalog #740000) were used for amplification and labeling using the Low RNA Input Linear Amplification Kit (Agilent) following the detailed protocol described in the kit manual.
|
| |
|
| Channel 2 |
| Source name |
HCC1937-BRCA1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BRCA1-transfected HCC1937
cell type: breast cancer cells
brca1 expression: yes
|
| Growth protocol |
Cell lines were cultured in DMEM medium supplemented with 10%FBS, 0.08% Fungizone and 100units/mL penicillin/streptomycin, and maintained at 37ºC in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cell lines using Trizol (Invitrogen) according to the instructions of the manufacturer.
|
| Label |
Cy5
|
| Label protocol |
500 ng of total RNA from samples and Universal Human Reference RNA (Stratagene, Catalog #740000) were used for amplification and labeling using the Low RNA Input Linear Amplification Kit (Agilent) following the detailed protocol described in the kit manual.
|
| |
|
| |
| Hybridization protocol |
For each hybridization, 1 μg Cyanine 3 labeled cRNA (reference) and 1 μg of Cyanine 5 labeled cRNA (samples) were mixed, fragmented, and hybridized at 65°C for 17 hours to an Agilent 4 × 44 K Whole Human Genome Oligo Microarray.
|
| Scan protocol |
Microarrays were scanned using an Agilent DNA microarray scanner.
|
| Data processing |
Agilent Feature Extraction software (version 9.5.3) was run on all array datasets using the GE2-v5_95_Feb07 protocol. Lowess and quantiles were applied for intra-array and between array normalization, respectively.
|
| |
|
| Submission date |
Jul 20, 2011 |
| Last update date |
Dec 24, 2011 |
| Contact name |
Beatriz Martinez |
| E-mail(s) |
bmartinez@cnio.es
|
| Organization name |
Spanish National Cancer Research Centre (CNIO)
|
| Department |
Human Cancer Genetics
|
| Street address |
Calle Melchor Fernandez Almagro 3
|
| City |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL6480 |
| Series (2) |
| GSE30821 |
Integration of BRCA1-mediated miRNA and mRNA signatures reveal miR-146a, miR-99b and miR-205 regulation of the TRAF2 and NFkB pathways (mRNA dataset) |
| GSE30822 |
Integration of BRCA1-mediated miRNA and mRNA signatures reveal miR-146a, miR-99b and miR-205 regulation of the TRAF2 and NFkB pathways |
|
