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Sample GSM2284870 Query DataSets for GSM2284870
Status Public on Apr 19, 2017
Title F5662Nsp, 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 0.004012 BB -0.652526 10.492647
AFFX-2315061 AB 0.003237 AB 0.153674 9.904387
AFFX-2315062 AA 0.004998 AA 0.543780 9.036589
AFFX-2315057 AB 0.004457 AB -0.199244 9.002191
AFFX-2315058 AA 0.034916 AA 0.731607 10.026888
AFFX-2315059 AA 0.002952 AA 0.783774 9.161593
AFFX-2315063 AA 0.014610 AA 0.806915 8.824402
AFFX-2315064 BB 0.015503 BB -0.749136 8.978298
AFFX-2315065 BB 0.013135 BB -0.673420 9.127868
AFFX-2315066 AB 0.007567 AB -0.035599 9.027660
AFFX-2315067 AB 0.000757 AB 0.055130 9.826370
AFFX-2315068 AA 0.037622 AA 0.835245 9.350936
AFFX-2315069 AA 0.009087 AA 0.840690 9.358422
AFFX-2315070 BB 0.009987 BB -0.740394 9.082941
AFFX-2315071 AB 0.014778 AB -0.049705 8.398850
AFFX-2315072 AB 0.010000 AB -0.080024 9.552608
AFFX-2315073 AB 0.008935 AB 0.106735 9.198898
AFFX-2315074 BB 0.023497 BB -0.648300 8.460501
AFFX-2315075 AA 0.008899 AA 0.726240 10.742472
AFFX-2315076 BB 0.033676 BB -0.623802 9.142273

Total number of rows: 262314

Table truncated, full table size 12191 Kbytes.




Supplementary file Size Download File type/resource
GSM2284870_F5662Nsp.CEL.gz 20.7 Mb (ftp)(http) CEL
GSM2284870_F5662Nsp.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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