|
| Status |
Public on Dec 03, 2010 |
| Title |
NBM_GE_1 |
| Sample type |
RNA |
| |
|
| Source name |
Normal CD34+ bone marrow cells
|
| Organism |
Homo sapiens |
| Characteristics |
sex (male.1_female.2): NA
bm_%blasts: NA
hemoglobin: NA
pb_%blasts: NA
platelets: NA
white_blood_cells: NA
age: NA
tet2: WT
idh1.idh2: WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted with Qiagen's Rneasy Plus Mini kit per manufacturer's instructions. cDNA synthesis carried out as previously described (Figueroa et al. PLoS One, 2008)
|
| Label |
Cy5
|
| Label protocol |
Random priming with 7-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.
|
| Description |
Sample name: NBM_1
|
| Data processing |
RMA normalization using the RMA algorithm found in the oligo package (version 1.8.3)(Carvalho et al.) in BioConductor
|
| |
|
| Submission date |
Oct 04, 2010 |
| Last update date |
May 08, 2012 |
| 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) |
| GSE24505 |
Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation |
|
