|
| Status |
Public on Aug 19, 2018 |
| Title |
Control JVM-2, 96 h |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
JVM-2-vehicle treated-96h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ACC-12
disease: Mantle cel lymphoma
cell type: Lymphoblast
subtype: Lymphoid
disease: Mantle cel lymphoma
|
| Treatment protocol |
cells were treated for 96 h with 0.001% DMSO in growth medium
|
| Growth protocol |
cells were grown in RPMI-1640 +10%FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy extraction kit. Evaluation of RNA quality was performed with the Agilent 2100 bioanalyzer and NanoDrop™ ND-1000 (Thermo Scientific).
|
| Label |
Cy5
|
| Label protocol |
Total RNA (0.5 μg) amplification and labeling with Cy3 or Cy5 was carried out using a modified Eberwein mRNA amplification procedure employing the MessageAmp™ aRNA amplification kit from Ambion (Applied Biosystems).
|
| |
|
| Channel 2 |
| Source name |
JVM-2-vehicle treated-96h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ACC-12
cell type: Lymphoblast
subtype: Lymphoid
|
| Treatment protocol |
cells were treated for 96 h with 0.001% DMSO in growth medium
|
| Growth protocol |
cells were grown in RPMI-1640 +10%FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy extraction kit. Evaluation of RNA quality was performed with the Agilent 2100 bioanalyzer and NanoDrop™ ND-1000 (Thermo Scientific).
|
| Label |
Cy3
|
| Label protocol |
Total RNA (0.5 μg) amplification and labeling with Cy3 or Cy5 was carried out using a modified Eberwein mRNA amplification procedure employing the MessageAmp™ aRNA amplification kit from Ambion (Applied Biosystems).
|
| |
|
| |
| Hybridization protocol |
Cy3 and Cy5 labeled cRNA for the control probes (Zea mays Zmmyb42 and Expansin) were added to the Cy3- and Cy5-labelled sample cRNA mixes and hybridized to microarrays according to the manufacturer’s instruction.
|
| Scan protocol |
Raw data were obtained using Agilent's DNA Microarray Scanner G2505B
Images were quantified using Agilent Feature Extraction software (v10.1)
|
| Description |
SI-107
JVM-2 VvsV, 96 h
|
| Data processing |
The raw fluorescence intensity data were processed using proprietary Oryzon Genomics SA Polyphemus software, which involves the following steps: 1. Spatial data compensation of the signals in the 2 channels based on the spike probes distributed over the array and generating signal at several discrete levels. 2. Noise filtering based on negative controls. 3. Data normalization by modified nonlinear Q-splines normalization method (Workman et al., 2002) and Log2(sample/control) value calculation without background correction. Differential expression assessment using robust statistics on the average of 3 technical replicates per gene oligo after removal of eventual outlier points (caused by dust or array imperfections). Criteria for outlier elimination are established automatically based on the intra-array technical variability of the signal distribution of the controls probes. The p-values are calculated after outlier elimination based on the absolute value of the regularized t-statistics (Baldi et al., 2001), which uses a Bayesian framework to derive the algorithm. Control probes have SPOTID ORY_C* and each is present in 2103 copies; gene oligos have SPOTID ORY_P* and each is present in triplicate, respectively, in the crossref file. The Agilent design file and AgilentOryzonRrossRef file are provided
|
| |
|
| Submission date |
Feb 06, 2017 |
| Last update date |
Aug 19, 2018 |
| Contact name |
Tamara Maes |
| Organization name |
Oryzon Genomics S.A.
|
| Department |
R&D
|
| Street address |
Carrer Sant Ferran 74
|
| City |
Cornella de Llobregat |
| State/province |
Barcelona |
| ZIP/Postal code |
08940 |
| Country |
Spain |
| |
|
| Platform ID |
GPL23032 |
| Series (1) |
| GSE94567 |
ORY-1001/RG6016 effect on leukemia cell lines |
|
