|
| Status |
Public on Nov 03, 2015 |
| Title |
Nalm6-WT3 |
| Sample type |
RNA |
| |
|
| Source name |
ALL leukemia cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: pre-B ALL leukemia cells
|
| Growth protocol |
10% FBS RPMI1640 + A/P + b-ME in 5% CO2, 37°C, change media every 2-3 days, cell density in 2x10^5 to 1x10^6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 5x10^6 Nalm6 cells were isoalted by using the RNeasy mini isolation kit (Qiagen) (n=3).
|
| Label |
Cy5
|
| Label protocol |
The 1ug of total RNA sample was amplied using the Ambion (Life Technologies) Amino Allyl MessageAmp II aRNA Amplification Kit (AM1753). Follow the manufacturer’s protocol for one cycle amplification. 4) Dye couple 15 ug of aRNA with Cy5 (GE Health Care #RPN5661), as appropriate, and subsequently purify according to the Ambion Kit instructions. A 10x dilution should have approximately 60 ng/ul of material with a range of 50-100 ng/ul
|
| |
|
| Hybridization protocol |
Reagents (Ambion AM8740) according the manufacturer’s instructions. Following fragmentation, dry samples down completely in a speed-vac. Resuspend each pair of samples in the appropriate Tracking Control and add Hybridization Solution Master Mix according to manufacturer’s instructions. (Roche NimbleGen).Incubate at 95C for 5 minutes, followed by 42C for 5 minutes. Attach appropriate mixer to the array and add hybridizations solution according to the manufacturer’s instructions. Hybridize with mixing in a MAUI hybridization instrument overnight at 42C.
|
| Scan protocol |
Dry the array slide completely. Place slide in a fresh tube and add 2.5 ml of Dye Saver. (Genisphere Inc). Coat the slide with DyeSaver by rotating the tube manually for 45 seconds. Spin at 700 RPM for 3 seconds down to remove excess DyeSaver.Remove from tube and allow to air dry briefly in a hood. Scan using Axon GenePix 4000B.
|
| Description |
The aRNA from the amplification of total RNA sample using the Ambion (Life Technologies) Amino Allyl MessageAmp II aRNA Amplification Kit (AM1753).
|
| Data processing |
The data from “pair” files were loaded into ArrayStar. RMA (Robust Multi-array Average) method with “quantile” type was used to normalize the data. Base 2 log signal values were transferred from the linear values. The three replicates of each probe were then averaged to be used as the gene expression values. The gene expression values of the probes in the same gene were averaged further.
|
| |
|
| Submission date |
Feb 11, 2013 |
| Last update date |
Nov 03, 2015 |
| Contact name |
chunhua song |
| E-mail(s) |
csong@hmc.psu.edu
|
| Phone |
717-531-1841
|
| Organization name |
Pennsyvania State University College of Medicine
|
| Department |
Pediatrics
|
| Street address |
500 University Drive
|
| City |
Hershey |
| State/province |
PA |
| ZIP/Postal code |
17033 |
| Country |
USA |
| |
|
| Platform ID |
GPL15143 |
| Series (2) |
| GSE44214 |
Gene expression profiling in Nalm6 ALL leukemia cells |
| GSE44218 |
Mechanism of Ikaros tumor suppression in Leukemia |
|
