|
| Status |
Public on Jun 05, 2015 |
| Title |
VM-CUB1 HOTAIR clone 20, rep3 |
| Sample type |
RNA |
| |
|
| Source name |
VM-CUB1 cells, stably transfected with HOTAIR
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: VM-CUB1
tumor type: urothelial cancer
|
| Treatment protocol |
Subsequent to transfection with HOTAIR plasmid or empty vector, stable transfected clones were isolated by treatment with puromycin.
|
| Growth protocol |
Cells were grown in DMEM supplemented with 10 % FCS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by means of RNeasy Mini Kit (Qiagen) according to manufacturer´s instruction. Ectopic overexpression was checked by QRT-PCR.
|
| Label |
biotin
|
| Label protocol |
Synthesis of cDNA and subsequent biotin labeling of cRNA was performed according to the manufacturers´ protocol (3´ IVT Express Kit; Affymetrix, Inc.). Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and biotin labelling of aRNA
|
| |
|
| Hybridization protocol |
After fragmentation labelled aRNA was hybridized to Affymetrix PrimeViewTM Human Gene Expression Microarrays for 16h at 45 °C, stained by strepatavidin/phycoerythrin conjugate and scanned as described in the manufacturers´ protocol
|
| Scan protocol |
Gene ChIP Scanner 3000 7G (Affymetrix Inc.); AGCC (Vers. 3.3)
|
| Description |
gene expression data from HOTAIR overexpressing VM-CUB1 cells
|
| Data processing |
Data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probeset were summarized by RMA after quantile normalization of probe level signal intensities across all samples to reduce inter-array variability . Input data pre-processing was concluded by baseline transformation to the median of all samples
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| |
|
| Submission date |
May 14, 2014 |
| Last update date |
Jun 05, 2015 |
| Contact name |
Karl Koehrer |
| E-mail(s) |
rene.deenen@hhu.de
|
| Organization name |
University of Duesseldorf
|
| Department |
BMFZ
|
| Lab |
GTL
|
| Street address |
Universitaetsstr. 1
|
| City |
Duesseldorf |
| ZIP/Postal code |
40225 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15207 |
| Series (1) |
| GSE57672 |
The long noncoding RNA HOTAIR has tissue and cell type dependent effects on HOX gene expression and phenotype of cancer cells |
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