|
| Status |
Public on Jun 12, 2017 |
| Title |
HaCaT_Keratinocyte_control_rep3_CTXSurival32.57 |
| Sample type |
RNA |
| |
|
| Source name |
HaCaT_Keratinocyte
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HaCaT
cell type: Keratinocyte
7 day cetuximab cell survival rate: 32.57
treated with: none (control)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the cell lines using Qiagen RNeasy Mini kit as directed (Qiagen, Valencia, CA). The quality and quantity of the RNA was determined using the Agilent RNA 6000 NanoLabChip kit and Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
biotin
|
| Label protocol |
The RNA was labeled with GeneChipR One-Cycle Target Labeling and Control Reagents.
|
| |
|
| Hybridization protocol |
Following fragmentation, the RNA was loaded on to the Affymetrix Human Genome U133 plus 2.0 GeneChip as directed (Affymetrix, Santa Clara, CA).
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G.
|
| Description |
940CC0127-20090811-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.
|
| Data processing |
fRMA normalization with R/Bioconductor package fRMA v1.7.2.
|
| |
|
| Submission date |
Feb 27, 2012 |
| Last update date |
Jun 12, 2017 |
| Contact name |
Elana Judith Fertig |
| E-mail(s) |
ejfertig@jhmi.edu
|
| Organization name |
Johns Hopkins University
|
| Department |
Oncology Quantitative Sciences
|
| Street address |
550 N Broadway, Suite 1101E
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21209 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE62027 |
HNSCC cell lines for CoGAPS matrix factorization algorithm identifies AP-2alpha as a feedback mechanism from therapeutic inhibition of the EGFR network |
|
