|
| Status |
Public on Sep 21, 2010 |
| Title |
FARAGE_1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
FARAGE Replicate #1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: DLBCL cell line
treatment group: Treated with control peptide
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rneasy Plus Mini kit (Qiagen)
|
| Label |
Cy3
|
| Label protocol |
Random priming with 9-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat # 05223547001)
|
| |
|
| Channel 2 |
| Source name |
FARAGE Replicate #1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: DLBCL cell line
treatment group: Treated with Bcl6 inhibitor peptide
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rneasy Plus Mini kit (Qiagen)
|
| Label |
Cy5
|
| Label protocol |
Random priming with 9-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat # 05223547001)
|
| |
|
| |
| Hybridization protocol |
See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details
|
| Scan protocol |
Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.
|
| Data processing |
Raw data files (pair files) were processed with Roche NimbleGen's version of the RMA algorithm (without background correction) in NimbleScan 2.3 software. Probe sets that showed at least a 1.8 log-ratio expression change from CP-treated samples after the administration of RI-BPI (BPI-treated samples) were used to generate a BPI gene expression (GE) signature. We subtracted the BPI-GE signature of BPI-responsive cells (OCI-Ly7, OCI-Ly10, Farage, SUDHL6 and SU-DHL4) from the BPI-GE signature of BPI-resistant cells (Pfeiffer, Toledo, OCI-Ly4 and Karpas422).
|
| |
|
| Submission date |
Sep 20, 2010 |
| Last update date |
Sep 20, 2010 |
| Contact name |
Maria Eugenia Figueroa |
| E-mail(s) |
mef162@miami.edu
|
| Organization name |
University of Miiami
|
| Department |
Human Genetics
|
| Lab |
Maria Figueroa
|
| Street address |
1501 NW 10th Ave, BRB 709A, Locator code C227
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL6602 |
| Series (1) |
| GSE24236 |
BCL6 repression of EP300 provides a basis for rational combinatorial therapy in diffuse large B cell lymphomas. |
|
