|
| Status |
Public on Aug 31, 2012 |
| Title |
ndf + progerin |
| Sample type |
RNA |
| |
|
| Source name |
human fibroblasts overexpressing progerin
|
| Organism |
Homo sapiens |
| Characteristics |
passage: 10
cell type: fibroblast
treatment: overexpressing progerin
cell line: GM00038
|
| Biomaterial provider |
Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM00038
|
| Treatment protocol |
When indicated, cells were grown in DMEM supplemented with either 10 nm farnesyltransferase inhibitor L-744832 (Biomol, Plymouth Meeting, PA, USA) or DMSO and 15% fetal bovine serum, 2 mm l-glutamine, 100 U mL−1 penicillin and 100 µg mL−1 streptomycin at 37 °C in 5% CO2, and 3% O2. Media was changed every 4 days.
|
| Growth protocol |
Primary dermal fibroblast cell line (GM00038) from healthy individual was obtained from the Coriell Cell Repository. Cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum, 2 mm l-glutamine, 100 U mL−1 penicillin and 100 µg mL−1 streptomycin at 37 °C in 5% CO2, and 3% O2. Cells seeded at 1.4 × 10exp5 per 100-mm-diameter dish were passaged when cultures reached 85% confluency.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from each fibroblast line at passage 10 using RNeasy kit from QIAGEN according to the manufacture’s protocol and quantitated by assessing absorbance at 260 and 280 nm using a NanoDropTM 1000 spectrophotometer.
|
| Label |
biotin
|
| Label protocol |
standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
Three micrograms of total RNA was then submitted to the University of Southern California Affymetrix MicroArray Core Facility at Children's Hospital Los Angeles for processing, chip hybridization, and scanning. Gene expression was analyzed on an Affimetrix gene chip Human Genome U133 Plus 2.0 Array,
|
| Scan protocol |
A Fluidics Station 400 (Affymetrix) was used to wash and stain the chips and fluorescence was detected using a G2500 GeneArray Scanner (Hewlett-Packard).
|
| Description |
Gene Expression data
|
| Data processing |
Raw data were analyzed initially using Microarray Suite version 5.0 (MAS 5.0, Affymetrix)
|
| |
|
| Submission date |
Aug 27, 2012 |
| Last update date |
Oct 17, 2012 |
| Contact name |
Lucio Comai |
| E-mail(s) |
comai@usc.edu
|
| Organization name |
University of Southern California
|
| Street address |
2250 Alcazar Street
|
| City |
Los Angeles |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE40404 |
Expression data from normal human fibroblasts expressing prelamin A or progerin, untreated or treated with farnesyltransferase inhibitor (FTI) |
|
