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Sample GSM2284866 Query DataSets for GSM2284866
Status Public on Apr 19, 2017
Title F4437Nsp, 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: Male
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 BB 0.030392 BB -0.660167 10.690834
AFFX-2315061 AB 0.011335 AB 0.077024 10.003839
AFFX-2315062 AA 0.037579 AA 0.552854 9.254166
AFFX-2315057 AB 0.026986 AB -0.100282 9.304039
AFFX-2315058 AB 0.002556 AB 0.177345 9.813467
AFFX-2315059 AA 0.035611 AA 0.778720 9.367367
AFFX-2315063 BB 0.003347 BB -0.807794 9.185199
AFFX-2315064 BB 0.015366 BB -0.693465 8.998886
AFFX-2315065 BB 0.011349 BB -0.594103 9.094145
AFFX-2315066 BB 0.011463 BB -0.625434 8.916615
AFFX-2315067 AB 0.012502 AB -0.008434 9.888478
AFFX-2315068 BB 0.010741 BB -0.612292 9.211707
AFFX-2315069 BB 0.029047 BB -0.864257 9.527000
AFFX-2315070 BB 0.007694 BB -0.770316 9.086160
AFFX-2315071 BB 0.015268 BB -0.735672 8.296925
AFFX-2315072 AA 0.015279 AA 0.665410 9.529214
AFFX-2315073 AA 0.008504 AA 0.706493 9.144516
AFFX-2315074 BB 0.011846 BB -0.573622 8.461583
AFFX-2315075 AA 0.004932 AA 0.674787 10.710677
AFFX-2315076 AB 0.017889 AB 0.093390 9.148533

Total number of rows: 262314

Table truncated, full table size 12194 Kbytes.




Supplementary file Size Download File type/resource
GSM2284866_F4437Nsp.CEL.gz 24.7 Mb (ftp)(http) CEL
GSM2284866_F4437Nsp.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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