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Sample GSM2284837 Query DataSets for GSM2284837
Status Public on Apr 19, 2017
Title F3404Nsp, 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

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 0.029096 AA 0.549351 10.539903
AFFX-2315061 AB 0.001258 AB 0.107077 9.762351
AFFX-2315062 AA 0.008379 AA 0.612423 9.147915
AFFX-2315057 AA 0.011279 AA 0.542227 8.996290
AFFX-2315058 BB 0.003005 BB -0.647496 9.358251
AFFX-2315059 BB 0.008141 BB -0.579466 8.911503
AFFX-2315063 BB 0.014731 BB -0.803518 9.268961
AFFX-2315064 AB 0.003703 AB 0.213979 9.070320
AFFX-2315065 AA 0.009766 AA 0.579920 8.943262
AFFX-2315066 AB 0.003432 AB 0.092130 8.946475
AFFX-2315067 AA 0.041365 AA 0.612454 10.069407
AFFX-2315068 AA 0.059040 AA 0.757971 8.905212
AFFX-2315069 AA 0.007993 AA 0.810577 9.325331
AFFX-2315070 AB 0.011271 AB -0.142866 9.119353
AFFX-2315071 AB 0.005686 AB -0.106551 8.299603
AFFX-2315072 AA 0.007924 AA 0.677640 9.512652
AFFX-2315073 AA 0.011736 AA 0.686897 9.119706
AFFX-2315074 AB 0.007347 AB 0.181230 8.553936
AFFX-2315075 BB 0.004272 BB -0.701835 10.642388
AFFX-2315076 BB 0.000218 BB -0.547940 8.962137

Total number of rows: 262314

Table truncated, full table size 12189 Kbytes.




Supplementary file Size Download File type/resource
GSM2284837_F3404Nsp.CEL.gz 25.7 Mb (ftp)(http) CEL
GSM2284837_F3404Nsp.brlmm.chp.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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