|
| Status |
Public on Jan 04, 2011 |
| Title |
JAK2 shRNA - 96 hr - mAdbID:97881 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Untreated (no DOX)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K1106
cell type: Primary Mediastinal B-cell Lymphoma
disease state: Primary Mediastinal B-cell Lymphoma Late Stage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol Total RNA
Extraction method: Trizol
Other: Total RNA was extracted using Trizol according to manufacturer's instructions (Invitrogen, Carlsbad, CA).
|
| Label |
cy3
|
| Label protocol |
Agilent Cy3 Labeling Protocol
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
|
| |
|
| Channel 2 |
| Source name |
JAK2 shRNA - 96 hr
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K1106
cell type: Primary Mediastinal B-cell Lymphoma
disease state: Primary Mediastinal B-cell Lymphoma Late Stage
|
| Treatment protocol |
Treatment type: shRNA transduction
Treatment time: 96 hr
In-vitro treatment: Knockdown by JAK2 shRNA after induction with doxycycline (20 ug/ml) for 96 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol Total RNA
Extraction method: Trizol
Other: Total RNA was extracted using Trizol according to manufacturer's instructions (Invitrogen, Carlsbad, CA).
|
| Label |
cy5
|
| Label protocol |
Agilent Cy5 Labeling Protocol
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
|
| |
|
| |
| Hybridization protocol |
Agilent Hybridization
Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).
|
| Scan protocol |
Agilent Scanning Protocol
Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays.
|
| Description |
mAdb experiment ID: 97881
|
| Data processing |
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.1.3.1). Spot values were normalized using the default linear-lowess normalization.
|
| |
|
| Submission date |
Mar 21, 2010 |
| Last update date |
Jan 04, 2011 |
| Contact name |
Louis M. Staudt |
| E-mail(s) |
[email protected]
|
| Phone |
301-402-1892
|
| Organization name |
National Cancer Institute
|
| Department |
Lymphoid Malignancies Branch
|
| Lab |
Louis M Staudt
|
| Street address |
9000 Rockville Pike, Bldg 10, Rm 4N114
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE20988 |
Cooperative Epigenetic Modulation by Cancer Amplicon Genes |
|
