|
| Status |
Public on Mar 14, 2011 |
| Title |
BJ-fib_2 |
| Sample type |
RNA |
| |
|
| Source name |
BJ fibroblast replicate 2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: bj-fib_2: BJ (CRL-2522) fibroblasts were purchased from ATCC.
|
| Biomaterial provider |
ATCC
|
| Growth protocol |
All fibroblasts were cultured in 5% CO2 and at 37°C in DMEM containing 15% FBS, 2 mM L-glutamine, 0.1 mM non-essential aminoacids, sodium Pyruvate, and 55 μM b-mercaptoethanol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen) followed by cDNA synthesis using High capability RNA-to-cDNA Mater Mix (Invitrogen).
|
| Label |
Biotin
|
| Label protocol |
The GeneChip microarray processing was performed by the Functional Genomica Core in the Institute for Research in Biomedicine (Barcelona, Spain) according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). The amplification and labeling were processed as indicated in Nugen protocol with 25ng starting RNA. For each sample, 3.75ug ssDNA were labeled and hybridized to the Affymetrix HG-U133 Plus 2.0 chips.
|
| |
|
| Hybridization protocol |
The GeneChip microarray processing was performed by the Functional Genomica Core in the Institute for Research in Biomedicine (Barcelona, Spain) according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). The amplification and labeling were processed as indicated in Nugen protocol with 25ng starting RNA. For each sample, 3.75ug ssDNA were labeled and hybridized to the Affymetrix HG-U133 Plus 2.0 chips.
|
| Scan protocol |
Expression signals were scanned on an Affymetrix GeneChip Scanner (7G upgrade). The data extraction was done by the Affymetrix GCOS software v.1.4.
|
| Data processing |
The statistical analysis of the data was performed using ArrayStar 3. Briefly, raw CEL files were imported together with gene annotation from NetAffix (from 11/13/2009) and normalized using RMA algorithm and quantile normalization. As both H9 ESC and HGPS-iPSC originate from female samples, and in order to check for any possible bias introduced by the X and Y chromosome-coded genes, we performed the same analysis with only autosome genes.
|
| |
|
| Submission date |
Oct 01, 2010 |
| Last update date |
Mar 14, 2011 |
| Contact name |
Stephanie Boue |
| Organization name |
CMRB
|
| Street address |
Dr Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE24487 |
Recapitulation of human premature aging by using iPSCs from Hutchinson-Gilford progeria syndrome |
|
