|
| Status |
Public on Feb 28, 2017 |
| Title |
MCF10A .WT.vs.H1047R - Replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
MCF10A
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10A
cell type: breast cancer
genotype: Wild-type
|
| Growth protocol |
MCF10A cells expressing JP1520-PIK3CA-WT(Addgene plasmid # 14570) and JP1520-PIK3CA-H1047R (Addgene plasmid # 14572) were generated and grown as described previously (Debnath et al., 2003; Hutti et al., 2012). Stable pools were generated by selection in 2ug/ml puromycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy RNA extraction kit (Qiagen) according to manufacturer's instruction.
|
| Label |
Cy3
|
| Label protocol |
10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label
|
| |
|
| Channel 2 |
| Source name |
MCF10A
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10A
cell type: breast cancer
genotype: activated PIK3CA mutant H1047R
|
| Growth protocol |
MCF10A cells expressing JP1520-PIK3CA-WT(Addgene plasmid # 14570) and JP1520-PIK3CA-H1047R (Addgene plasmid # 14572) were generated and grown as described previously (Debnath et al., 2003; Hutti et al., 2012). Stable pools were generated by selection in 2ug/ml puromycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy RNA extraction kit (Qiagen) according to manufacturer's instruction.
|
| Label |
Cy5
|
| Label protocol |
10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label
|
| |
|
| |
| Hybridization protocol |
Scanned on an Agilent SureScan Microarray Scanner.
|
| Scan protocol |
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
|
| Description |
biological replicate 1 of 3
|
| Data processing |
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and Linear-Lowess normalization.
|
| |
|
| Submission date |
Jan 11, 2017 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Antoine Elias Karnoub |
| E-mail(s) |
[email protected]
|
| Phone |
617-735-2082
|
| Organization name |
Beth Israel Deaconess Medical Center and Harvard Medical School
|
| Department |
Pathology
|
| Lab |
Karnoub Lab
|
| Street address |
3 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL16699 |
| Series (1) |
| GSE93422 |
Pentraxin-3 is a PI 3-Kinase Effector that Regulates Stem-Cell-Like Traits in Basal-Like Breast Cancer |
|
| Relations |
| Reanalyzed by |
GSE113533 |
