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Sample GSM2284916 Query DataSets for GSM2284916
Status Public on Apr 19, 2017
Title F5686Sty, 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_Sty
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 GPL3720
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

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
CONTRAST
STRENGTH

Data table
ID_REF VALUE CONFIDENCE FORCED CALL CONTRAST STRENGTH
AFFX-2315060 BB 0.013743 BB -0.786683 10.756789
AFFX-2315061 AB 0.018864 AB 0.024588 9.451889
AFFX-2315062 AB 0.010013 AB -0.058646 8.870574
AFFX-2315057 BB 0.221141 BB -0.625573 8.591798
AFFX-2315058 AB 0.007125 AB 0.212602 10.128260
AFFX-2315059 AB 0.008276 AB 0.221620 9.174832
AFFX-2315063 AB 0.019344 AB -0.152038 9.042672
AFFX-2315064 AB 0.406781 AB 0.212643 7.463038
AFFX-2315065 AA 0.046815 AA 0.668745 8.537916
AFFX-2315066 BB 0.027237 BB -0.706574 8.532515
AFFX-2315067 BB 0.008762 BB -0.680443 9.778246
AFFX-2315068 AA 0.060711 AA 0.814779 8.760066
AFFX-2315069 AA 0.007885 AA 0.700587 8.212824
AFFX-2315070 AB 0.016495 AB -0.248853 8.512571
AFFX-2315071 BB 0.045416 BB -0.799538 8.170899
AFFX-2315072 BB 0.034711 BB -0.835725 9.340675
AFFX-2315073 AB 0.037121 AB 0.065757 8.564243
AFFX-2315074 BB 0.092527 BB -0.538953 7.562982
AFFX-2315075 BB 0.157618 BB -0.745381 9.547930
AFFX-2315076 AB 0.024888 AB 0.019869 9.199707

Total number of rows: 238354

Table truncated, full table size 11082 Kbytes.




Supplementary file Size Download File type/resource
GSM2284916_F5686Sty.CEL.gz 19.2 Mb (ftp)(http) CEL
GSM2284916_F5686Sty.brlmm.chp.gz 3.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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