|
| Status |
Public on Sep 14, 2012 |
| Title |
URE-shControl-2 |
| Sample type |
RNA |
| |
|
| Source name |
URE cell line
|
| Organism |
Mus musculus |
| Characteristics |
vector: luciferase control
infection protocol: GFP+ URE cells infected with luciferase control shRNA
cell line: URE
|
| Treatment protocol |
URE cells were infected with short-hairpin-containing pSIH1-H1-copGFP lentiviral vector (System Biosciences, Mountain View, CA) containing either nucleotide sequences targeting luciferase (shControl) or HLX (shHLX). URE cells were transduced with short-hairpin-containing lentivirus for Hlx knockdown study and then GFP-positive cells were sorted. After culture for several days, RNA was extracted from 1X10E5 cells by RNeasy Micro Kit (Qiagen).
|
| Growth protocol |
Cultured in M5300+10%FBS containing 15%WEHI supernatant and 15%BHK supernatant.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 1X10E5 cells using the RNeasy Micro Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
10ng RNA was used for amplification of cDNA by Nugen Ovation pico WTA system following the manufacture’s protocol. labeling was performed by GeneChip WT terminal labeling kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridization kit; GeneChip Hybridization Wash and Stain Kit (Affymetrix). GeneChip; Affymetrix Mouse Gene 1.0ST microarrays (Affymetrix)
|
| Scan protocol |
GeneChip Scanner 3000 7G system (Affymetrix).
|
| Description |
sorted GFP+ URE cells infected with luciferase control shRNA
|
| Data processing |
Microarray data was normalized with the RMA algorithm of Affymetrix Power Tools (v 1.178). Log2-transformed signals are listed. A t-test with Welch approximation for unequal group variances with p-values based on t-distribution was performed with a cutoff of p<0.1 in Multiple Experiment Viewer v.4 pilot2 (http://www.tm4.org/mev/) (PMID: 16939790). Subsequently, the probes with -log10(p) value <0.05 and a mean difference > 0.5 were considered differentially expressed and used for further analysis.
|
| |
|
| Submission date |
Mar 14, 2011 |
| Last update date |
Sep 14, 2012 |
| Contact name |
Boris Bartholdy |
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Cell Biology
|
| Street address |
1300 Morris Park Ave
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (2) |
| GSE27939 |
Identification of differentially regulated genes upon shRNA-mediated knock-down of HLX in the URE leukemia cell line |
| GSE27947 |
Identification of differentially regulated genes in hematopoietic stem cells and URE leukemia cell line |
|
