|
| Status |
Public on Sep 11, 2007 |
| Title |
bone_marrow_02 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
human genomic female DNA: Promega G1521
|
| Organism |
Homo sapiens |
| Characteristics |
control: pooled female DANN
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For DNA isolation archieved bone marrow cells were washed in PBS and DNA was isolated with QIAmp DNA Blood Midi Kit (Qiagen, Hilden, Germany) according to the protocol of the manufacturer.
|
| Label |
Cy3
|
| Label protocol |
Labelling: 1.) Digestion of genomic DNA: Mix the following components on ice in the order stated: 15µl Nuclease free water, 5µl 10x Buffer C (Promega), 2.5µl Alu I (10u/ul)( Promega P/N R6281), 2.5µl Rsa I (10U/ul) (Promega P/N R6371). Dilute 2-5 ug genom
|
| |
|
| Channel 2 |
| Source name |
bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
WHO classification: 5q- syndrome, bm blasts (%): 1, sex/age at diagnosis (years): female/70, karyotype: 46,XX,del(5)(q13q33)[17]/46,XX[3], % del5q (FISH): 57, % del5q (karyogram)85
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For DNA isolation archieved bone marrow cells were washed in PBS and DNA was isolated with QIAmp DNA Blood Midi Kit (Qiagen, Hilden, Germany) according to the protocol of the manufacturer.
|
| Label |
Cy5
|
| Label protocol |
Labelling: 1.) Digestion of genomic DNA: Mix the following components on ice in the order stated: 15µl Nuclease free water, 5µl 10x Buffer C (Promega), 2.5µl Alu I (10u/ul)( Promega P/N R6281), 2.5µl Rsa I (10U/ul) (Promega P/N R6371). Dilute 2-5 ug genom
|
| |
|
| |
| Hybridization protocol |
Hybridization: 1. Add the following components in the order indicated to reaction tubes containing 150 l of purified Cy5- and Cy3-labeled sample mixture: 50µl Cot-1 DNA (1.0 mg/ml) (Invitrogen 15279-011), 50µl Agilent 10x Blocking Reagent, 250µl Agilent
|
| Scan protocol |
Scanned on Agilent Array scanner G2505B following manufacturers recommendations, scan resolution: 10µm.
Images were quantified using Feature Extraction Software (version A.7.5.1, June 2004) (Agilent Technologies).
|
| Description |
MDC vs control genomic DNA
|
| Data processing |
Linear&LOWESS normalized log10 ratios (red/green) (standard settings of Feature Extraction Software), converted to log2 ratios (test/reference) afterwards
|
| |
|
| Submission date |
Aug 17, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Brigitte Royer-Pokora |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf
|
| Street address |
Universitätsstr. 1
|
| City |
Duesseldorf |
| ZIP/Postal code |
40225 |
| Country |
Germany |
| |
|
| Platform ID |
GPL2879 |
| Series (1) |
| GSE8804 |
Precise Delination of 5q-Breakpoints and Detection of Hidden Aberrations in patients with MDS using Array CGH |
|
