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Sample GSM2284896 Query DataSets for GSM2284896
Status Public on Apr 19, 2017
Title F3476Sty, 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_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 0.008690 AB -0.093594 11.081082
AFFX-2315061 AB 0.000372 AB 0.144984 9.789552
AFFX-2315062 BB 0.008179 BB -0.740548 9.202764
AFFX-2315057 AB 0.023548 AB -0.196885 8.852200
AFFX-2315058 AB 0.000353 AB 0.185864 10.244519
AFFX-2315059 AA 0.021694 AA 0.830088 9.317448
AFFX-2315063 AA 0.021167 AA 0.744232 8.743454
AFFX-2315064 AA 0.044118 AA 0.596307 7.899083
AFFX-2315065 AA 0.015980 AA 0.550881 8.523501
AFFX-2315066 BB 0.022327 BB -0.725316 8.596591
AFFX-2315067 AA 0.004681 AA 0.691557 10.277658
AFFX-2315068 AB 0.028804 AB 0.265198 8.887773
AFFX-2315069 AA 0.016088 AA 0.680480 8.128123
AFFX-2315070 BB 0.042085 BB -0.639286 8.639128
AFFX-2315071 AB 0.015911 AB -0.041905 8.113827
AFFX-2315072 AA 0.028712 AA 0.798679 9.469768
AFFX-2315073 AB 0.051358 AB 0.251745 8.713205
AFFX-2315074 BB 0.024167 BB -0.493818 7.827765
AFFX-2315075 AB 0.016937 AB -0.069670 9.708367
AFFX-2315076 AB 0.040832 AB -0.192319 9.278297

Total number of rows: 238354

Table truncated, full table size 11083 Kbytes.




Supplementary file Size Download File type/resource
GSM2284896_F3476Sty.CEL.gz 19.9 Mb (ftp)(http) CEL
GSM2284896_F3476Sty.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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