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Sample GSM2284835 Query DataSets for GSM2284835
Status Public on Apr 19, 2017
Title F3292Nsp, 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 0.002927 AA 0.632178 10.475245
AFFX-2315061 AB 0.001870 AB 0.127342 9.740383
AFFX-2315062 AA 0.032397 AA 0.536069 9.197582
AFFX-2315057 BB 0.009537 BB -0.626304 9.224012
AFFX-2315058 AA 0.003512 AA 0.680393 9.910740
AFFX-2315059 AB 0.017242 AB 0.307818 8.900298
AFFX-2315063 AB 0.000005 AB -0.113188 9.100044
AFFX-2315064 AB 0.012540 AB 0.145057 9.051424
AFFX-2315065 AA 0.046118 AA 0.510276 8.769539
AFFX-2315066 BB 0.008921 BB -0.622992 8.785180
AFFX-2315067 AB 0.000830 AB 0.068352 9.865715
AFFX-2315068 AB 0.009480 AB 0.253075 9.312720
AFFX-2315069 BB 0.000949 BB -0.850534 9.333905
AFFX-2315070 AA 0.012315 AA 0.773927 8.935783
AFFX-2315071 BB 0.017584 BB -0.696283 8.282290
AFFX-2315072 AB 0.000748 AB -0.035401 9.385590
AFFX-2315073 BB 0.004460 BB -0.639703 9.010039
AFFX-2315074 AB 0.005500 AB 0.139466 8.289331
AFFX-2315075 AB 0.005260 AB -0.036741 10.543212
AFFX-2315076 AB 0.002890 AB 0.078760 9.046846

Total number of rows: 262314

Table truncated, full table size 12192 Kbytes.




Supplementary file Size Download File type/resource
GSM2284835_F3292Nsp.CEL.gz 20.8 Mb (ftp)(http) CEL
GSM2284835_F3292Nsp.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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