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Sample GSM2284841 Query DataSets for GSM2284841
Status Public on Apr 19, 2017
Title F3434Nsp, 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 0.014072 AA 0.541483 10.379120
AFFX-2315061 BB 0.004323 BB -0.763644 9.677984
AFFX-2315062 BB 0.001344 BB -0.726510 9.165499
AFFX-2315057 BB 0.013054 BB -0.652316 9.264006
AFFX-2315058 AA 0.032162 AA 0.616188 9.783793
AFFX-2315059 AA 0.012891 AA 0.748921 9.237866
AFFX-2315063 AA 0.006780 AA 0.797727 9.125282
AFFX-2315064 BB 0.003538 BB -0.709298 8.861403
AFFX-2315065 AA 0.009480 AA 0.617146 8.761504
AFFX-2315066 AB 0.001567 AB 0.067995 8.868727
AFFX-2315067 BB 0.022797 BB -0.586849 9.711493
AFFX-2315068 AB 0.007417 AB 0.271926 9.191586
AFFX-2315069 AA 0.002307 AA 0.808871 9.120343
AFFX-2315070 BB 0.006275 BB -0.776318 9.047266
AFFX-2315071 BB 0.023360 BB -0.714819 8.330068
AFFX-2315072 AB 0.007828 AB -0.002431 9.584896
AFFX-2315073 BB 0.007394 BB -0.588394 9.112191
AFFX-2315074 AB 0.000913 AB 0.115442 8.428188
AFFX-2315075 BB 0.011621 BB -0.722826 10.725509
AFFX-2315076 BB 0.045162 BB -0.470038 8.878546

Total number of rows: 262314

Table truncated, full table size 12191 Kbytes.




Supplementary file Size Download File type/resource
GSM2284841_F3434Nsp.CEL.gz 21.9 Mb (ftp)(http) CEL
GSM2284841_F3434Nsp.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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