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Sample GSM2284865 Query DataSets for GSM2284865
Status Public on Apr 19, 2017
Title F4317Nsp, 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 AB 0.004678 AB -0.138531 10.434928
AFFX-2315061 AA 0.036743 AA 0.839259 10.015194
AFFX-2315062 AB 0.002077 AB -0.079724 9.165467
AFFX-2315057 AA 0.002856 AA 0.527787 8.790120
AFFX-2315058 AB 0.004759 AB 0.159590 9.669873
AFFX-2315059 BB 0.006661 BB -0.662582 9.007408
AFFX-2315063 BB 0.064024 BB -0.820215 9.465961
AFFX-2315064 AB 0.001615 AB 0.304437 9.154883
AFFX-2315065 AB 0.002051 AB -0.115920 8.979200
AFFX-2315066 AB 0.009754 AB 0.026246 9.114483
AFFX-2315067 AB 0.017531 AB 0.028145 10.011956
AFFX-2315068 AB 0.015882 AB 0.287721 9.295653
AFFX-2315069 AB 0.016517 AB -0.224710 9.486127
AFFX-2315070 AB 0.007379 AB -0.119508 9.076033
AFFX-2315071 AB 0.011981 AB -0.147394 8.326390
AFFX-2315072 AB 0.002208 AB -0.052493 9.460654
AFFX-2315073 AB 0.022526 AB 0.149711 9.315470
AFFX-2315074 BB 0.017884 BB -0.620230 8.494380
AFFX-2315075 AB 0.000485 AB 0.037847 10.628662
AFFX-2315076 AA 0.020434 AA 0.602232 9.111086

Total number of rows: 262314

Table truncated, full table size 12191 Kbytes.




Supplementary file Size Download File type/resource
GSM2284865_F4317Nsp.CEL.gz 21.6 Mb (ftp)(http) CEL
GSM2284865_F4317Nsp.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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