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Sample GSM2284880 Query DataSets for GSM2284880
Status Public on Apr 19, 2017
Title F3292Sty, 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 AA 0.001212 AA 0.664871 10.770586
AFFX-2315061 AB 0.002412 AB 0.178451 9.731911
AFFX-2315062 AA 0.000323 AA 0.675793 9.044072
AFFX-2315057 BB 0.043119 BB -0.614216 9.288785
AFFX-2315058 AA 0.027802 AA 0.702447 10.474205
AFFX-2315059 AB 0.003954 AB 0.198297 9.429324
AFFX-2315063 AB 0.000015 AB -0.206774 9.291750
AFFX-2315064 AB 0.018420 AB 0.212259 8.274065
AFFX-2315065 AA 0.021709 AA 0.570512 8.841993
AFFX-2315066 BB 0.007009 BB -0.695821 8.880560
AFFX-2315067 AB 0.003966 AB 0.138755 10.230637
AFFX-2315068 AB 0.009908 AB 0.176319 9.266061
AFFX-2315069 BB 0.038918 BB -0.786118 8.775507
AFFX-2315070 AA 0.007439 AA 0.657399 8.642905
AFFX-2315071 BB 0.021285 BB -0.803494 8.578058
AFFX-2315072 AB 0.003781 AB 0.016692 9.982041
AFFX-2315073 BB 0.001921 BB -0.655133 9.012726
AFFX-2315074 AB 0.001896 AB 0.063487 8.225054
AFFX-2315075 AB 0.006149 AB -0.011568 10.070353
AFFX-2315076 AB 0.001455 AB -0.064670 9.529929

Total number of rows: 238354

Table truncated, full table size 11085 Kbytes.




Supplementary file Size Download File type/resource
GSM2284880_F3292Sty.CEL.gz 21.0 Mb (ftp)(http) CEL
GSM2284880_F3292Sty.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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