|
| Status |
Public on Jul 20, 2015 |
| Title |
lnc3-1st |
| Sample type |
RNA |
| |
|
| Source name |
K562 cells treated with anti-luciferase shRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: leukemia cell line K562
shRNA: control
|
| Treatment protocol |
K562 cells were treated with lentivirally-expressed anti-luciferase or anti-Bcr-Abl shRNAs
|
| Growth protocol |
K562 cells were maintained in RPMI1640 containing 10% fetal calf serum (FCS) supplemented with penicillin (100 U/ml) and streptomycin (100 U/ml). Cells were grown in a humidified incubator at 37℃ and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using TRIzol reagent (Invitrogen, Carlsbad, CA).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000 B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).
|
| Description |
K562 cells infected with lentivirally-expressed anti-luciferase shRNA
|
| Data processing |
Scanned images (TIFF format) were imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. All mRNA and lncRNA level files were imported into Agilent GeneSpring Software (version 11.0) for further analysis. lncRNAs and mRNAs that at least 6 out of 6 samples have values greater than or equal to lower cut-off: 50.0 were chosen for differentially expressed lncRNAs and mRNAs screening. Differentially expressed lncRNAs and mRNAs were identified through Volcano Plot filtering.
|
| |
|
| Submission date |
Nov 14, 2012 |
| Last update date |
Jul 20, 2015 |
| Contact name |
Guijie Guo |
| E-mail(s) |
guojie1125@163.com
|
| Organization name |
Institute of Microbiology, Chinese Academy of Sciences (CAS)
|
| Street address |
NO.1 Beichen West Road, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL14715 |
| Series (1) |
| GSE42269 |
A Tumor Suppressor Function of LncRNA-X in Bcr-Abl-induced Tumorigenesis |
|
