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Sample GSM2284906 Query DataSets for GSM2284906
Status Public on Apr 19, 2017
Title F3506Sty, 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: Male
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 AB 0.015673 AB 0.011239 11.064330
AFFX-2315061 AB 0.006400 AB 0.201690 9.850467
AFFX-2315062 AB 0.000909 AB -0.063728 9.030622
AFFX-2315057 AB 0.020102 AB -0.209176 8.909829
AFFX-2315058 BB 0.004594 BB -0.737232 10.023748
AFFX-2315059 AB 0.019380 AB 0.357439 9.402737
AFFX-2315063 AB 0.004127 AB -0.220215 9.174854
AFFX-2315064 BB 0.210857 BB -0.256750 7.711695
AFFX-2315065 AB 0.017679 AB -0.169662 8.868928
AFFX-2315066 AB 0.007774 AB 0.027333 8.629020
AFFX-2315067 AB 0.000048 AB 0.106150 10.155690
AFFX-2315068 AA 0.011463 AA 0.823857 8.976501
AFFX-2315069 AB 0.010964 AB -0.111599 8.246047
AFFX-2315070 AB 0.003397 AB -0.219549 8.596272
AFFX-2315071 AA 0.008276 AA 0.682311 8.033377
AFFX-2315072 BB 0.005555 BB -0.774293 9.447351
AFFX-2315073 AB 0.000836 AB 0.127726 8.879944
AFFX-2315074 BB 0.022594 BB -0.619877 8.014097
AFFX-2315075 AB 0.024901 AB -0.157228 9.721954
AFFX-2315076 AB 0.002748 AB -0.103809 9.405465

Total number of rows: 238354

Table truncated, full table size 11081 Kbytes.




Supplementary file Size Download File type/resource
GSM2284906_F3506StyOK.CEL.gz 19.9 Mb (ftp)(http) CEL
GSM2284906_F3506StyOK.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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