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Sample GSM2284905 Query DataSets for GSM2284905
Status Public on Apr 19, 2017
Title F3497Sty, 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_Sty
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 GPL3720
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 0.005821 AB -0.145367 10.777682
AFFX-2315061 BB 0.000013 BB -0.785835 9.610756
AFFX-2315062 BB 0.003465 BB -0.730437 9.042934
AFFX-2315057 AA 0.002335 AA 0.602841 8.916691
AFFX-2315058 AB 0.004318 AB 0.196396 10.382411
AFFX-2315059 AA 0.009772 AA 0.788558 9.425116
AFFX-2315063 AA 0.010032 AA 0.814326 9.297891
AFFX-2315064 AB 0.001858 AB 0.203411 8.155769
AFFX-2315065 BB 0.048506 BB -0.715767 8.965357
AFFX-2315066 AB 0.002047 AB 0.034956 8.924086
AFFX-2315067 AA 0.095788 AA 0.583612 10.339294
AFFX-2315068 AA 0.013751 AA 0.836344 9.196888
AFFX-2315069 BB 0.027791 BB -0.810789 8.751901
AFFX-2315070 BB 0.020527 BB -0.764998 8.838952
AFFX-2315071 AA 0.018017 AA 0.742881 8.455087
AFFX-2315072 AB 0.033989 AB -0.147412 10.078825
AFFX-2315073 AB 0.018293 AB 0.028222 9.200962
AFFX-2315074 AA 0.001593 AA 0.657920 7.986251
AFFX-2315075 AB 0.000945 AB -0.048766 9.978019
AFFX-2315076 BB 0.016145 BB -0.705068 9.619753

Total number of rows: 238354

Table truncated, full table size 11083 Kbytes.




Supplementary file Size Download File type/resource
GSM2284905_F3497Sty.CEL.gz 21.6 Mb (ftp)(http) CEL
GSM2284905_F3497Sty.brlmm.chp.gz 3.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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