|
| Status |
Public on Feb 04, 2014 |
| Title |
TF-1alpha Transwell Mono-culture - 4 hr |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
TF-1alpha Transwell Mono-culture - 4 hr
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone marrow
cell line: TF-1alpha
cell type: CD34+/CD38- myeloid leukemia cells
disease state: myeloid leukemia
other: Cells were harvested after 4 hours of mono-culture.
|
| Treatment protocol |
In-vitro treatment: AML cell line, TF-1alpha, cells were mono-cultured in a 1-um Transwell system (BD Biosciences, San Jose, CA USA). TF-1alpha cells were harvested and RNA extracted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sample Extraction Protocol
Other: Total RNA was purified using miRNA Easy Kit (Qiagen). The RNA concentration was measured using a Nano Drop ND-1000 Spectrophotometer (Nano Drop Technologies, Wilmington, DE, USA) and RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
|
| Label |
cy5
|
| Label protocol |
Cy5 Labeling Protocol
Other: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit.
|
| |
|
| Channel 2 |
| Source name |
Universal Human Reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
other: Stratagene(TM)UHR RNA Sample Pooling: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.
|
| Biomaterial provider |
Stratagene (La Jolla, CA)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Strategene UHR RNA Extraction
Other: not available
|
| Label |
cy3
|
| Label protocol |
Cy3 Labeling Protocol
Other: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit.
|
| |
|
| |
| Hybridization protocol |
Agilent Hybridization Protocol
Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).
|
| Scan protocol |
Agilent Scanning Protocol
Other: Images of the arrays were acquired using a microarray scanner Scan G2505B and image analysis was performed using Scan Control software version 9.5 (Agilent Technologies). The images were extracted using the Feature Extraction Software (Agilent Technologies).
|
| Description |
No additional information.
|
| Data processing |
Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Agilent Technologies). Spot values were normalized using the default linear-lowess normalization. Partek Genomic Suite 6.4 (Partek Inc., St. Louis, MO, USA) and Ingenuity Pathway Analysis website (http://www.ingenuity.com, Ingenuity System Inc., Redwood City, CA, USA) were used for further data analysis.
|
| |
|
| Submission date |
Apr 01, 2013 |
| Last update date |
Feb 04, 2014 |
| Contact name |
PING JIN |
| E-mail(s) |
PJIN@CC.NIH.GOV
|
| Organization name |
CC/DTM/NIH
|
| Department |
DTM
|
| Lab |
CCE
|
| Street address |
9000 ROCKVILLE PIKE
|
| City |
BETHESDA |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE45663 |
Leukemia Cell Lines Induce Changes in Bone Marrow Stromal Cells |
|
