|
| Status |
Public on Aug 13, 2016 |
| Title |
IVLBCL #3 spleen |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
IVLBCL PDX #3, spleen
|
| Organism |
Homo sapiens |
| Characteristics |
disease: intravascular large B-cell lymphoma (IVLBCL)
age: 77
Sex: Male
mouse's organs with engrafted tumors: spleen
|
| Growth protocol |
The patient derived xenograft IVLBCL models were established from primary patient bone marrow samples.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from engrafted IVLBCL tumor cells in mouse organs using QIAamp DNA Blood Mini Kit according to the manufacturer's protocol (QIAGEN, Venlo, Netherlands)
|
| Label |
Cy5
|
| Label protocol |
DNA was digested with AluI and RsaI restriction enzymes. Sample DNA was labeled with Cy5-dUTP. As reference, mixture of DNA from normal healthy men was labeled with Cy3-dUTP.
|
| |
|
| Channel 2 |
| Source name |
Mixture of DNA from healthy individuals
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: Male
|
| Growth protocol |
The patient derived xenograft IVLBCL models were established from primary patient bone marrow samples.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from engrafted IVLBCL tumor cells in mouse organs using QIAamp DNA Blood Mini Kit according to the manufacturer's protocol (QIAGEN, Venlo, Netherlands)
|
| Label |
Cy3
|
| Label protocol |
DNA was digested with AluI and RsaI restriction enzymes. Sample DNA was labeled with Cy5-dUTP. As reference, mixture of DNA from normal healthy men was labeled with Cy3-dUTP.
|
| |
|
| |
| Hybridization protocol |
Test and reference labeled DNA samples were hybridized at 65°C for 40 hours on the 2x400K microarray glass (G4448A, Agilent, Palo Alto, CA) , and washed with Agilent Wash Buffers 1 and 2.
|
| Scan protocol |
The slideglass was scanned on an Agilent G2565BA scanner (Agilent, Palo Alto, CA) using a resolution of 3μm per pixel and 100% of the photomultiplicator for both signals.
|
| Description |
IVL07IVL03sp
|
| Data processing |
The background biases in the log2 ratio values of the CGH analysis data were adjusted according to standard statistical methods. Specifically, the correlation bias with GC content of the corresponding clone sequence was first removed. Then the probe-specific bias was also removed, where the bias at each probe was estimated by the running mean of the adjacent 10 probed in the both slides.
|
| |
|
| Submission date |
Aug 13, 2015 |
| Last update date |
Aug 13, 2016 |
| Contact name |
KAZUYUKI SHIMADA |
| E-mail(s) |
kshimada@med.nagoya-u.ac.jp
|
| Organization name |
NAGOYA UNIVERSITY
|
| Department |
HEMATOLOGY AND ONCOLOGY
|
| Street address |
65, Tsurumai-cho, Showa-ku
|
| City |
NAGOYA |
| ZIP/Postal code |
4668550 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19387 |
| Series (2) |
| GSE72027 |
Array CGH analysis for intravascular large B-cell lymphoma (IVLBCL) |
| GSE72028 |
Gene expression profiling and array CGH analysis for intravascular large B-cell lymphoma (IVLBCL) |
|
