|
| Status |
Public on Jan 31, 2017 |
| Title |
Multiple myeloma. Pair 5. Diagnosis. [methylation] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
MM patient_diagnosis
|
| Organism |
Homo sapiens |
| Characteristics |
subject condition: Multiple myeloma (MM) patient
sample pair id: pair 5
gender: Male
age (yr): 69
patient status: diagnosis
tissue: Bone marrow
cell type: CD 138+ plasma cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The genomic DNA was extracted from frozen bone marrow samples with QIAmp DNA Mini Kit (Qiagen, 16 Valencia, CA, USA) following the manufacturer’s instructions
|
| Label |
Cy3
|
| Label protocol |
Samples were denatured and labeled in parallel with Cy3 for the test group and Cy5 for the control group, each through a random priming method, using Klenow fragments (NimbleGen Dual-Color DNA Labeling Kit, Roche NimbleGen, Inc., Madison, WI, USA) following the manufacturer protocol
|
| |
|
| Channel 2 |
| Source name |
MM patient_diagnosis_input
|
| Organism |
Homo sapiens |
| Characteristics |
subject condition: Multiple myeloma (MM) patient
sample pair id: pair 5
gender: Male
age (yr): 69
patient status: diagnosis
tissue: Bone marrow
cell type: CD 138+ plasma cells
sample type: Input
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The genomic DNA was extracted from frozen bone marrow samples with QIAmp DNA Mini Kit (Qiagen, 16 Valencia, CA, USA) following the manufacturer’s instructions
|
| Label |
Cy5
|
| Label protocol |
Samples were denatured and labeled in parallel with Cy3 for the test group and Cy5 for the control group, each through a random priming method, using Klenow fragments (NimbleGen Dual-Color DNA Labeling Kit, Roche NimbleGen, Inc., Madison, WI, USA) following the manufacturer protocol
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed according to the instructions in the NimbleGen Array User Guide
|
| Scan protocol |
Scanning was performed according to the instructions in the NimbleGen Array User Guide
|
| Description |
P5D_1416
|
| Data processing |
Arrays were processed using Nimblegen's standard protocol. Batch-effects were removed using ComBat R package. Quantile normalization was done using the affy R package.
|
| |
|
| Submission date |
Feb 03, 2016 |
| Last update date |
Jan 31, 2017 |
| Contact name |
Norma C. Gutiérrez |
| E-mail(s) |
[email protected]
|
| Phone |
+34923291384
|
| Organization name |
Centro de Investigación del Cáncer de Salamanca
|
| Department |
Hematologia
|
| Lab |
12
|
| Street address |
Campus Miguel de Unamuno
|
| City |
Salamanca |
| State/province |
Salamanca |
| ZIP/Postal code |
37007 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17148 |
| Series (2) |
| GSE77537 |
Integrative analysis of DNA copy number, DNA methylation and gene expression in multiple myeloma reveals alterations related to relapse [DNA methylation] |
| GSE77540 |
Integrative analysis of DNA copy number, DNA methylation and gene expression in multiple myeloma reveals alterations related to relapse |
|
