|
| Status |
Public on Jun 30, 2014 |
| Title |
BxPC3_JMJD3KD_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
human pancreatic cancer cell line BxPC3 transfected with vector expressing shJMJD3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BxPC3
cell type: pancreatic cancer
transfected vector: shJMJD3-expressing
|
| Treatment protocol |
BxPC3 cells were transfected with either control vector or vector expressing shJMJD3.
|
| Growth protocol |
Cells were grown in RPMI with 10% fetal bovine serum, and maintained at 37C in 5% CO2 in a humidified environment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells with the RNeasy mini kit (Qiagen) following the manufacturer’s instructions, and was quantified by Nanodrop.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 500ng RNA using the Quick Amp Labeling Kit (One colour, Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).
|
| |
|
| Hybridization protocol |
Labeled cRNA was incubated with Blocking agent and Fragmentation buffer (Agilent Gene Expression Hybridization Kit) for 30min at 60°C. GE Hybridization Buffer HI-RPM was then added to the mixture. Samples were applied to microarrays using hybridization chambers and hybridized at 65°C for 16h. After hybridization, slides were washed sequentially with Agilent Gene Expression Wash Buffer.
|
| Scan protocol |
The hybridized array slides were scanned on an Agilent Microarray Scanner. Scanned images were quantified using Agilent Feature Extraction software (ver. 10.5.1.1).
|
| Description |
Gene expression after transfection of vector expressing shJMJD3 in BxPC3 cells.
|
| Data processing |
Microarray signal and background information were retrieved using Agilent Feature Extraction software (ver. 10.5.1.1). Extracted intensities were background-corrected and normalized by the quantile normalization method using statistical software R (http://www.R-project.org) and the Bioconductor package “Agi4x44PreProcess” (Pedro Lopez-Romero) (http://www.bioconductor.org/packages/2.3/bioc/html/Agi4x44PreProcess.html). Probes were filtered based on the Quality Flags provided by Agilent FE using the function "filter.probes" in the "Agi4x44PreProcess" package. Replicated probes were summarized using the function "summarize.probe".
|
| |
|
| Submission date |
Mar 24, 2011 |
| Last update date |
Jun 30, 2014 |
| Contact name |
Keisuke Yamamoto |
| E-mail(s) |
[email protected]
|
| Organization name |
NYU School of Medicine
|
| Department |
Radiation Oncology
|
| Street address |
550 First Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE28155 |
Loss of histone demethylase KDM6B enhances aggressiveness of pancreatic cancer through downregulation of C/EBPα |
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