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Sample GSM2284857 Query DataSets for GSM2284857
Status Public on Apr 19, 2017
Title F3491Nsp, 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 BB 0.008805 BB -0.679488 10.449119
AFFX-2315061 AB 0.016929 AB 0.184471 9.635729
AFFX-2315062 AB 0.028094 AB -0.260315 9.066850
AFFX-2315057 AA 0.008995 AA 0.471789 8.736402
AFFX-2315058 AB 0.239734 AB 0.329634 9.475090
AFFX-2315059 AB 0.009499 AB 0.276334 8.903434
AFFX-2315063 BB 0.003287 BB -0.769904 9.072033
AFFX-2315064 AA 0.079941 AA 0.818253 8.852065
AFFX-2315065 AB 0.002235 AB -0.077730 9.089650
AFFX-2315066 AA 0.038650 AA 0.737343 8.596591
AFFX-2315067 BB 0.107805 BB -0.379003 9.366468
AFFX-2315068 AA 0.016660 AA 0.730291 9.115096
AFFX-2315069 AB 0.027309 AB 0.054635 8.995276
AFFX-2315070 BB 0.182788 BB -0.617036 8.737928
AFFX-2315071 AB 0.213259 AB -0.149926 7.483122
AFFX-2315072 AB 0.004510 AB -0.008811 9.283562
AFFX-2315073 AB 0.038775 AB 0.175993 8.765575
AFFX-2315074 BB 0.034056 BB -0.576484 8.110606
AFFX-2315075 AB 0.002103 AB 0.030583 10.727082
AFFX-2315076 AB 0.019140 AB 0.049685 8.809731

Total number of rows: 262314

Table truncated, full table size 12190 Kbytes.




Supplementary file Size Download File type/resource
GSM2284857_F3491Nsp.CEL.gz 19.4 Mb (ftp)(http) CEL
GSM2284857_F3491Nsp.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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