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Sample GSM2284907 Query DataSets for GSM2284907
Status Public on Apr 19, 2017
Title F3507Sty, 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 AA 0.002640 AA 0.636781 10.743777
AFFX-2315061 AB 0.004378 AB 0.142422 9.923419
AFFX-2315062 BB 0.001170 BB -0.735214 9.109269
AFFX-2315057 AA 0.001797 AA 0.608896 8.854851
AFFX-2315058 BB 0.005782 BB -0.664835 10.094061
AFFX-2315059 BB 0.006272 BB -0.724140 9.171329
AFFX-2315063 AB 0.012704 AB -0.215276 9.513309
AFFX-2315064 BB 0.010992 BB -0.384387 7.910862
AFFX-2315065 AA 0.022432 AA 0.664175 8.670819
AFFX-2315066 AB 0.001636 AB 0.010174 8.746581
AFFX-2315067 BB 0.002587 BB -0.690606 10.006815
AFFX-2315068 BB 0.000315 BB -0.724647 8.939993
AFFX-2315069 AA 0.005270 AA 0.716411 8.458073
AFFX-2315070 BB 0.256326 BB -0.560523 8.235851
AFFX-2315071 AB 0.001774 AB -0.172646 8.400772
AFFX-2315072 AA 0.000003 AA 0.815690 9.721222
AFFX-2315073 AB 0.003382 AB 0.110698 8.825005
AFFX-2315074 BB 0.001498 BB -0.568809 7.955154
AFFX-2315075 AB 0.000034 AB -0.071012 9.925726
AFFX-2315076 BB 0.000250 BB -0.711458 9.487365

Total number of rows: 238354

Table truncated, full table size 11081 Kbytes.




Supplementary file Size Download File type/resource
GSM2284907_F3507Sty.CEL.gz 22.1 Mb (ftp)(http) CEL
GSM2284907_F3507Sty.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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