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Sample GSM2284847 Query DataSets for GSM2284847
Status Public on Apr 19, 2017
Title F3462Nsp, 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 0.007959 AA 0.623698 10.350757
AFFX-2315061 AA 0.014897 AA 0.838523 9.551641
AFFX-2315062 AB 0.044725 AB -0.266182 8.979154
AFFX-2315057 AB 0.079938 AB -0.271161 8.847521
AFFX-2315058 AB 0.008470 AB 0.141398 9.640913
AFFX-2315059 AA 0.010327 AA 0.778587 9.087278
AFFX-2315063 AB 0.042157 AB -0.010361 8.643852
AFFX-2315064 AB 0.206353 AB 0.360647 8.569089
AFFX-2315065 AB 0.014028 AB -0.031469 8.869544
AFFX-2315066 AA 0.030452 AA 0.678674 8.572753
AFFX-2315067 AA 0.052297 AA 0.585417 9.638474
AFFX-2315068 AB 0.019355 AB 0.270891 9.032315
AFFX-2315069 AB 0.015499 AB 0.012846 9.061419
AFFX-2315070 BB 0.036105 BB -0.680288 8.862558
AFFX-2315071 AB 0.024551 AB -0.171954 7.953169
AFFX-2315072 AA 0.029276 AA 0.685133 9.215849
AFFX-2315073 AA 0.064582 AA 0.681921 8.774439
AFFX-2315074 BB 0.088082 BB -0.427606 8.159520
AFFX-2315075 AB 0.008735 AB 0.029010 10.450384
AFFX-2315076 BB 0.108965 BB -0.606065 8.633194

Total number of rows: 262314

Table truncated, full table size 12190 Kbytes.




Supplementary file Size Download File type/resource
GSM2284847_F3462NspOK.CEL.gz 19.1 Mb (ftp)(http) CEL
GSM2284847_F3462NspOK.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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