|
| Status |
Public on Jan 01, 2014 |
| Title |
NSCL/P sample 4 |
| Sample type |
RNA |
| |
|
| Source name |
dental pulp stem cells extracted from deciduos tooth
|
| Organism |
Homo sapiens |
| Characteristics |
condition: Non-syndromic cleft lip/palate (NSCL/P)
tissue: decidous teeth dental pulp
gender: female
|
| Treatment protocol |
No specific treatment was used in cells cultures. Growing cells were used in the media described above.
|
| Growth protocol |
Cells were cultured in DMEM-F12 (Life Technologies) supplemented with 15% Foetal Bovine Serum (HyClone), 1% Non-essential aminoacids solution (Life Technologies), 1% penicillin-streptomycin solution (Life Technologies), in a humidified incubator at 37oC and 5% CO2. For storage, cells were frozen in medium containing 90% FBS and 10% DMSO (LGC Biotecnologia). Protocols are also described in Bueno et al, 2011 Stem Cell Reviews and Reports.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation was performed with NucleoSpin RNA II kit (Macherey-Nagel), following manufacturer’s recommendations. RNA quality and concentration were assessed using Nanodrop 1000 and agarose gel electrophoresis. Only RNA samples with absorbance ratio 260/280 > 1.8, preserved rRNA ratio (28S/18S) and no signs of degradation were used.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip®Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and hybridized for 16 hr in the Affymetrix Hybridization Oven 640.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
|
| Description |
gene expression data from dental pulp stem cells extracted from deciduos tooth
|
| Data processing |
Data were analyzed with Expression Console (Affymetrix) and normalized by RMA method.
|
| |
|
| Submission date |
Nov 28, 2012 |
| Last update date |
Jan 01, 2014 |
| Contact name |
Lucas Alvizi |
| E-mail(s) |
[email protected]
|
| Phone |
+551130919910
|
| Organization name |
University of Sao Paulo
|
| Department |
Genetics and Evolutionary Biology
|
| Lab |
Human Development Genetics Lab
|
| Street address |
Rua do Matao 277
|
| City |
Sao Paulo |
| State/province |
Sao Paulo |
| ZIP/Postal code |
05508-090 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE42589 |
Susceptibility to DNA damage as a molecular mechanism for non-syndromic cleft lip and palate |
|
