|
| Status |
Public on May 01, 2014 |
| Title |
AML1-ETO 3 days 1 |
| Sample type |
RNA |
| |
|
| Source name |
CD34+ cells_AML1-ETO 3 days
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary human CD34+ cells
transduced/nucleofected with: AML1-ETO
culture time (hrs): 72
|
| Treatment protocol |
Preactivated primary human CD34+ cells were nucleofected with pTracer-CMV/Bsd constructs expressing the fusion proteins or empty vector as described Takeda A, Goolsby C, Yaseen NR (2006) Cancer Res 66: 6628–6637.). Cells were cultured at 2x10^5/mL in complete cytokine medium (Takeda A, Goolsby C, Yaseen NR (2006) Cancer Res 66: 6628–6637.) for 3.5 h. GFP+ cells were sorted using MoFlo sorter and cultured at 105/mL in complete cytokine medium for 2.5 h before RNA isolation.
|
| Growth protocol |
GFP-sorted cells were collected and snap-frozen 6 h after nucleofection, or 3 and 8 days after retroviral transduction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolated using the RNeasy mini kit (Qiagen) was submitted to the Siteman Cancer Center Laboratory for Clinical Genomics. Target was prepared using linear amplification protocol for the 6 h time point and standard protocol for the 3 and 8 day time points and hybridized to Affymetrix HG-U133 Plus 2.0 GeneChip arrays according to manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
amplified cDNA was fragmentated and labeled using Encore Biotin Module V2 according to manufactures instructions. www.nugeninc.com/nugen/index.cfm/products/pl/target-preparation/encore-biotin-module/
|
| |
|
| Hybridization protocol |
Affymetrix Hybridization protocol
|
| Scan protocol |
arrays were scanned in the Affymetrix Genearray 2500 scanner to generate flourescent images, as described in Affymetrix GeneChip protocol.
|
| Description |
eto_3d_1
|
| Data processing |
Cell intesity files (CEL files) were generated in the Genechip Command Console Software (AGCC), (Affymetrix, Santa Clara, CA, USA)
intensity where obtained after processing with the justRMA() function from the affy package in R
|
| |
|
| Submission date |
Apr 30, 2014 |
| Last update date |
May 19, 2014 |
| Contact name |
Anmaar Abdul-Nabi |
| E-mail(s) |
[email protected]
|
| Phone |
3127310297
|
| Organization name |
Washington University in Saint louis
|
| Department |
Pathology and Immunology
|
| Lab |
Nabeel Yaseen
|
| Street address |
660 South Euclid Avenue. PO box 8118
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE57194 |
In Vitro Transformation of Primary Human CD34+ Cells by AML Fusion Oncogenes: Early Gene Expression Profiling Reveals Possible Drug Target in AML |
|
