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Sample GSM2284856 Query DataSets for GSM2284856
Status Public on Apr 19, 2017
Title F3488Nsp, 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 0.009305 BB -0.649507 10.444187
AFFX-2315061 BB 0.011900 BB -0.793648 9.439166
AFFX-2315062 AB 0.043779 AB -0.236863 8.919633
AFFX-2315057 AB 0.029013 AB -0.135930 8.849586
AFFX-2315058 AA 0.047447 AA 0.676597 9.661815
AFFX-2315059 AB 0.073929 AB 0.336697 8.732483
AFFX-2315063 BB 0.022350 BB -0.796932 8.907202
AFFX-2315064 AA 0.023104 AA 0.808926 8.990335
AFFX-2315065 AB 0.020387 AB -0.077749 8.822330
AFFX-2315066 AA 0.017692 AA 0.653557 8.743248
AFFX-2315067 BB 0.002810 BB -0.523962 9.590446
AFFX-2315068 AB 0.031071 AB 0.155713 8.900500
AFFX-2315069 AB 0.016578 AB -0.141810 9.038637
AFFX-2315070 AB 0.027476 AB -0.164472 8.623035
AFFX-2315071 AB 0.036810 AB -0.111806 7.846382
AFFX-2315072 AA 0.033382 AA 0.646273 9.196463
AFFX-2315073 AA 0.031509 AA 0.684555 8.857200
AFFX-2315074 AB 0.041881 AB 0.153815 8.092325
AFFX-2315075 AA 0.012531 AA 0.642962 10.508856
AFFX-2315076 AB 0.031481 AB 0.002971 8.769365

Total number of rows: 262314

Table truncated, full table size 12191 Kbytes.




Supplementary file Size Download File type/resource
GSM2284856_F3488Nsp.CEL.gz 24.1 Mb (ftp)(http) CEL
GSM2284856_F3488Nsp.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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