|
| Status |
Public on May 31, 2018 |
| Title |
P2/PE2 r3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Parental treated with everolimus
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: parental clear cell renal cell carcinoma ccRCC-PCSC (HKPCSC -human parental kidney cancer stem cells)
treatment: 3 day treatment with everolimus
|
| Treatment protocol |
HKCSC and HPKCSC cell lines were treated with everolimus for 3 days. HPKCSC cells were treated with dose near half of IC50 calculated for HPKCSC cell line (4µM). More resistant HKCSC cells were treated with 1 µM higher dose than HPKCSC (5µM).
|
| Growth protocol |
Human kidney cancer stem cells (HKCSC) and human parental kidney cancer stem cells (HPKCSC) of two histological types – clear cell renal cell carcinoma (ccRCC) and papillary renal cell carcinoma (ppRCC) were purchased from Cellprogen (Torrance, CA, USA).HKCSC were cultured in Human Kidney Cancer Stem Cell Complete Medium with Serum, and HKPCSC in Human Kidney (Parental) Stem Cell Complete Media with Serum (as per manufactures protocol).All cell lines were cultured in standard incubation culture conditions.Cells were in the logarithmic growth phase at the beginning of all experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA isolated using High Pure Isolation Kit (Roche Life Science), according to the manufacturer’s protocol.
|
| Label |
Cy5
|
| Label protocol |
according to the manufacturer's protocol (Protocol for use with Agilent Gene Expression oligo microarrays Version 6.9.1, August 2015)
|
| |
|
| Channel 2 |
| Source name |
Parental untreated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: parental clear cell renal cell carcinoma ccRCC-PCSC (HKPCSC -human parental kidney cancer stem cells)
treatment: 3 days of growth after passage
|
| Treatment protocol |
HKCSC and HPKCSC cell lines were treated with everolimus for 3 days. HPKCSC cells were treated with dose near half of IC50 calculated for HPKCSC cell line (4µM). More resistant HKCSC cells were treated with 1 µM higher dose than HPKCSC (5µM).
|
| Growth protocol |
Human kidney cancer stem cells (HKCSC) and human parental kidney cancer stem cells (HPKCSC) of two histological types – clear cell renal cell carcinoma (ccRCC) and papillary renal cell carcinoma (ppRCC) were purchased from Cellprogen (Torrance, CA, USA).HKCSC were cultured in Human Kidney Cancer Stem Cell Complete Medium with Serum, and HKPCSC in Human Kidney (Parental) Stem Cell Complete Media with Serum (as per manufactures protocol).All cell lines were cultured in standard incubation culture conditions.Cells were in the logarithmic growth phase at the beginning of all experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA isolated using High Pure Isolation Kit (Roche Life Science), according to the manufacturer’s protocol.
|
| Label |
Cy3
|
| Label protocol |
according to the manufacturer's protocol (Protocol for use with Agilent Gene Expression oligo microarrays Version 6.9.1, August 2015)
|
| |
|
| |
| Hybridization protocol |
according to the manufacturer's protocol (Protocol for use with Agilent Gene Expression oligo microarrays Version 6.9.1, August 2015)
|
| Scan protocol |
Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).
|
| Description |
Parental/ Parental treated with everolimus, 2 biological replicate, 3 technical
|
| Data processing |
Microarray data normalization, quality control, principal component analysis, and filtered on flags were performed using GeneSpring GX 13.0 (Agilent, Santa Clara, CA, USA). Statistical analysis of the gene expression microarray data was performed using moderate T-test and multiple testing corrected with Bonferonni FWER algorithm. The statistical significance was assessed at p<0.05 and fold change cut off >2.0 (up-/down-regulated).
|
| |
|
| Submission date |
Nov 13, 2017 |
| Last update date |
May 31, 2018 |
| Contact name |
Anna Justyna Kornakiewicz |
| E-mail(s) |
anna.kornakiewicz@gmail.com
|
| Organization name |
School of Molecular Medicine
|
| Street address |
Ksiecia Trojdena 2a
|
| City |
Warsaw |
| ZIP/Postal code |
02-091 |
| Country |
Poland |
| |
|
| Platform ID |
GPL20844 |
| Series (1) |
| GSE106819 |
Effect of everolimus on clear cell renal cell carcinoma (ccRCC) cell lines - parental and stem cells |
|
