|
| Status |
Public on Apr 19, 2017 |
| Title |
F3413Nsp, Patient |
| Sample type |
genomic |
| |
|
| Source name |
OOMMSC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Orbicularis Oris Muscle Mesenchymal Stem Cells Primary Cultures
phenotype: Nonsyndromic cleft lip/palate (NSCL/P)
gender: Female
|
| Treatment protocol |
No specific treatment was used in cells cultures.
|
| Growth protocol |
We established OOMMSC primary cultures according to previously published protocol [Bueno et al. 2009] and expanded to 70-90% confluence.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA isolation was performed with NucleoSpin tissue kit (Macherey-Nagel), following manufacturer’s recommendations. DNA quality and concentration were assessed using Nanodrop 1000 and agarose gel electrophoresis.
|
| Label |
Biotin
|
| Label protocol |
Following restriction enzyme digestion, biotin labeled DNA was prepared according to the Affymetrix protocol from 250ng of starting DNA (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005).
|
| |
|
| Hybridization protocol |
Mapping 500K arrays were washed and stained in the Affymetrix Fluidics Station 450, then hybridized according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using an Affymetrix model 640 hybridization oven.
|
| Scan protocol |
Mapping 500K arrays were scanned according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using a GeneChip Scanner 3000 7G.
|
| Description |
Hybridized to 250K_Nsp
|
| Data processing |
CEL-Files were analyzed using the BRLMM-algorithm, implemented in the Genotyping Console software (Affymetrix, USA), to produce genotype calls, stored in the corresponding CHP-Files.
Genotypes primarily generated under Genome version hg18 (GRCh36.1) were converted to hg19 with UCSC LiftOver tool.
|
| |
|
| Submission date |
Aug 18, 2016 |
| Last update date |
Apr 19, 2017 |
| Contact name |
Cibele Masotti |
| 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 |
São Paulo |
| ZIP/Postal code |
05508-090 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL3718 |
| Series (2) |
| GSE85814 |
MRPL53, a New Candidate Gene for Orofacial Clefting, Identified Using an eQTL Approach [SNP array] |
| GSE85817 |
MRPL53, a New Candidate Gene for Orofacial Clefting, Identified Using an eQTL Approach |
|
