|
| Status |
Public on Mar 04, 2008 |
| Title |
SEB-1 treated biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
sebocyte cell line, SV-40 immortalized, 13-cis retinoic acid treated
|
| Organism |
Homo sapiens |
| Characteristics |
sebocytes cultured from M, 55, normal preauricular sebaceous glands and SV-40 immortalized
|
| Treatment protocol |
SEB-1 sebocytes (p23) were treated in triplicate with 0.1 uM 13-cis RA or vehicle (DMSO) control for 72 hours. Each culture plate was considered an independent sample.
|
| Growth protocol |
SEB-1 sebocytes were cultured in standard culture medium according to established procedures (Thiboutot et al, 2003).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated and DNase I treated using the Rneasy Kit (Qiagen, Valencia, CA). RNA was quantified using a spectrophotometer. Approximately 2 micrograms of total RNA from each sample was used to generate double-stranded cDNA using a T7-oligo (dT) primer.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA, produced through in vitro transcription
|
| |
|
| Hybridization protocol |
Biotinylated cRNA, produced through in vitro transcription, was fragmented and hybridized to an Affymetrix human U95Av2 microarray.
|
| Scan protocol |
The arrays were processed on a Gene Chip Fluidics Station 450 and scanned on a Affymetrix GeneChip Scanner (Santa Clara, CA).
|
| Description |
Gene expression data from SEB-1 cell line with 72hr, 0.1uM 13-cis retinoic acid treatment
|
| Data processing |
The expression values were normalized by using the R-Affy package from Bioconductor version 1.1 to remove background noise and non-biologival variations among arrays. The background noise was removed from the PM probe intensities using the "RMA" method. Normalization was performed using the quantile normalization method (Bolstad et. al., 2003). To remove the effects of outlier probes and sumerize probe intensities within one probe set to a single expression value, the "Tukey Biweight" method was applied to the background adjusted, normalized PM intensities and not the PM-MM, because it is believed that MM intensities reflect background noise as well as probe-specific signals. Significant gene expression alterations were identified using the computer software: Significance Analysis of Microarrays (Tusher et. al.,2001).
|
| |
|
| Submission date |
Feb 07, 2008 |
| Last update date |
Mar 16, 2009 |
| Contact name |
Diane M Thiboutot |
| E-mail(s) |
dthiboutot@psu.edu
|
| Organization name |
The Pennsylvannia State University College of Medicine
|
| Department |
Department of Dermatology; Jake Gittlen Res. Fnd.
|
| Street address |
500 University Drive
|
| City |
Hershey |
| State/province |
PA |
| ZIP/Postal code |
17033 |
| Country |
USA |
| |
|
| Platform ID |
GPL8300 |
| Series (2) |
| GSE10432 |
13-cis retinoic acid treatment of human sebocytes (SEB-1) |
| GSE10434 |
Retinoic acid effect on sebocytes and the skin |
|
