|
| Status |
Public on Jan 26, 2011 |
| Title |
Primary patient sample MMRC0389_1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
CD138+ plasma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD138+ plasma
disease state: tumor
|
| Treatment protocol |
No post collection treatment was performed.
|
| Growth protocol |
After informed consent bone marrow aspirates were collected in sodium citrate tubes at MMRC member institutions and shipped by overnight courier to the MMRC Tissue Bank (Scottsdale, Arizona). White blood cells were collected after red cell lysis using ACK reagent. Plasma cells were selected using CD138 and the RoboSep (StemCell Technologies) as per the manufacturers protocol. The purified plasma cells were lysed in 1 ml of TRIzol Reagent (Life Technologies).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA was extracted from the TRIzol suspension using the manufacturers protocol and subsequently DNA was isolated from the remaining fraction as suggested by the manufacturer. The isolated DNA was treated with RNaseA for 15 minutes and digested with proteinase K overnight. Subsequently, the DNA was cleaned-up with two phenol-chloroform extractions and one final chlorophorm extraction before the DNA was precipitated with EtOH and NaOAc. The purified DNA was quantified on a Nanodrop Spectrophotometer
|
| Label |
Cy5
|
| Label protocol |
1.2 ug of DNA was digested with DNase I for 12 minutes. The digested DNA was labeled using the BioPrime Array CGH Genomic Labeling Module with Amersham cUTP-CY dyes from GE Healthcare (Reference=CY3 and Tumor=CY5). The labeled DNA was purified using Vivaspin 500 columns
|
| |
|
| Channel 2 |
| Source name |
Promega XX Control DNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample_type: reference
|
| Treatment protocol |
No post collection treatment was performed.
|
| Growth protocol |
After informed consent bone marrow aspirates were collected in sodium citrate tubes at MMRC member institutions and shipped by overnight courier to the MMRC Tissue Bank (Scottsdale, Arizona). White blood cells were collected after red cell lysis using ACK reagent. Plasma cells were selected using CD138 and the RoboSep (StemCell Technologies) as per the manufacturers protocol. The purified plasma cells were lysed in 1 ml of TRIzol Reagent (Life Technologies).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA was extracted from the TRIzol suspension using the manufacturers protocol and subsequently DNA was isolated from the remaining fraction as suggested by the manufacturer. The isolated DNA was treated with RNaseA for 15 minutes and digested with proteinase K overnight. Subsequently, the DNA was cleaned-up with two phenol-chloroform extractions and one final chlorophorm extraction before the DNA was precipitated with EtOH and NaOAc. The purified DNA was quantified on a Nanodrop Spectrophotometer
|
| Label |
Cy3
|
| Label protocol |
1.2 ug of DNA was digested with DNase I for 12 minutes. The digested DNA was labeled using the BioPrime Array CGH Genomic Labeling Module with Amersham cUTP-CY dyes from GE Healthcare (Reference=CY3 and Tumor=CY5). The labeled DNA was purified using Vivaspin 500 columns
|
| |
|
| |
| Hybridization protocol |
Labeled DNA was hybridized to Agilent Human Genome 244A CGH Microarrays and arrays were washed as recommended by the manufacturer
|
| Scan protocol |
Microarrays were scanned with a Agilent GA2565BA or GA2505C scanner at 5um resolution and 16-bit color depth
|
| Description |
Primary patient sample
Untreated cells
|
| Data processing |
Data was extracted from the aquired TIFF files using Agilent Feature Extraction v10.5.1.1 using the CGH_105_Dec08 extraction protocol. Data were subsequently corrected for batch-to-batch variation and for wave artifact.
|
| |
|
| Submission date |
Jan 25, 2011 |
| Last update date |
Jan 26, 2011 |
| Contact name |
Michael Anthony Chapman |
| E-mail(s) |
mchapman@broadinstitute.org
|
| Organization name |
Broad Institute
|
| Street address |
7 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL9128 |
| Series (2) |
| GSE26849 |
MMRC aCGH reference collection |
| GSE26863 |
MMRC expression and aCGH reference collection |
|
