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Status |
Public on Feb 04, 2014 |
Title |
TF-1 + BMSCs in Direct Co-culture - 4 hr |
Sample type |
RNA |
|
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Channel 1 |
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.
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|
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Channel 2 |
Source name |
TF-1 + BMSCs in Direct Co-culture - 4 hr
|
Organism |
Homo sapiens |
Characteristics |
tissue: Bone marrow cell line: TF-1 cell type: CD34+/CD38+ myeloid leukemia cells (TF-1) and Bone marrow derived stromal cells (BMSCs) disease state: myeloid leukemia other: Cells were harvested after 4 hours of co-culture.
|
Treatment protocol |
In-vitro treatment: AML cell line, TF-1, cells were co-cultured with BMSCs from healthy donors. The two populations were cultured together in direct contact in the same well without any membrane separation. The cells from both populations were harvested together 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.
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|
|
|
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).
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Description |
No additional information.
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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.
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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 |
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