|
| Status |
Public on May 10, 2011 |
| Title |
HKI-004-other |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
breast tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
chek2 1100delc mutation status: other
er status (1=positive, o=negative): 1
family history of breast cancer (1=familial case, 0=sporadic case): 1
histological subtype: ductal
nqo1 rs1800566 genotype: NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sections of frozen tumor tissues (roughly 10 – 100 mg) were submerged in liquid nitrogen and homogenized using a mechanical homogenizer, after which the tissue powder was dissolved in 4 ml of TrizolTM. The RNA was then separated into an aqueous phase by adding 800 ml of chloroform followed by centrifugation at 12,000 g at four degrees centigrade for 15 min. Subsequent RNA extraction and purification was performed using the Qiagen RNeasy RNA purification kit (Qiagen Inc., CA, USA).
|
| Label |
cy3
|
| Label protocol |
Fluorescently labeled cDNA targets for hybridization were prepared according to manufacturers' instructions using the Corning Pronto Plus system 6.
|
| |
|
| Channel 2 |
| Source name |
Universal Human RNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference
disease state: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sections of frozen tumor tissues (roughly 10 – 100 mg) were submerged in liquid nitrogen and homogenized using a mechanical homogenizer, after which the tissue powder was dissolved in 4 ml of TrizolTM. The RNA was then separated into an aqueous phase by adding 800 ml of chloroform followed by centrifugation at 12,000 g at four degrees centigrade for 15 min. Subsequent RNA extraction and purification was performed using the Qiagen RNeasy RNA purification kit (Qiagen Inc., CA, USA).
|
| Label |
cy5
|
| Label protocol |
Fluorescently labeled cDNA targets for hybridization were prepared according to manufacturers' instructions using the Corning Pronto Plus system 6.
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized and washed as previously described (PMID:17334996).
|
| Scan protocol |
Arrays were scanned with Agilent Microarray Scanner (Agilent Technologies) and quality controlled using the GenePix 4.1.1.4 software (Axon instruments)
|
| Data processing |
Background correction was done with the normexp method recommended by [PMID: 17720982]. Data was normalized first within arrays with the print-tip loess method and subsequently between arrays with the quantile method. Measurements of replicate reporters were averaged.
|
| |
|
| Submission date |
Oct 14, 2010 |
| Last update date |
May 10, 2011 |
| Contact name |
Taru A Muranen |
| E-mail(s) |
taru.a.muranen@helsinki.fi
|
| Organization name |
Helsinki University Central Hospital
|
| Department |
Department of Obstetrics and Gynecology
|
| Lab |
Heli Nevanlinna
|
| Street address |
Haartmaninkatu
|
| City |
Helsinki |
| ZIP/Postal code |
00029 |
| Country |
Finland |
| |
|
| Platform ID |
GPL11052 |
| Series (2) |
| GSE24697 |
Breast tumors from CHEK2 1100delC mutation carriers: genomic landscape and clinical implications (GEX) |
| GSE24707 |
Breast tumors from CHEK2 1100delC mutation carriers: genomic landscape and clinical implications |
|
