Dataset features

Specifications


Application: SNP array data analysis, aCGH data analysis
Number of samples: 34
Release date: Oct 1 2012
Last update date: May 17 2017
Access: Public
Chemicals: Nucleotides
Dataset link Genome-wide haplotyping of human single cells

Experimental Protocol


In total 12 amplified single human lymphoblastoid cell DNA samples, 3 amplified single human blastomere DNA samples and 19 non-amplified genomic DNA samples extracted from blood were analyzed by 250K Nsp I SNP arrays (GEO accession number GPL3718). The non-amplified genomic DNA samples extracted from blood were derived from 19 different persons belonging to 4 different families. The sample names of these 19 samples are respectively Family1_Individual1, Family1_mother, Family1_father, Family1_MaternalGrandmother, Family2_Individual2, Family2_mother, Family2_father, Family2_MaternalGrandmother, Family2_MaternalGrandfather, Family3_Individual3, Family3_Individual4, Family3_mother, Family3_father, Family3_MaternalGrandmother, Family3_MaternalGrandfather, Family4_mother, Family4_father, Family4_PaternalGrandmother, Family4_PaternalGrandfather. These 19 non-amplified genomic DNA samples extracted from blood were genotyped using the dynamic model algorithm embedded in the ‘GeneChip Genotyping Analysis Software (GTYPE) version 4.1 (Affymetrix)’ using a homozygous and heterozygous calling threshold of 0.12. The 12 amplified single lymphoblastoid cell DNA samples were derived from Epstein Barr virus transformed lymphoblastoid cell lines (EBV-line) of four different persons. Three amplified single lymphoblastoid cell DNA samples from individual “Family1_Individual1”, three amplified single lymphoblastoid cell DNA samples from individual “Family2_Individual2”, three amplified single lymphoblastoid cell DNA samples from individual “Family3_Individual3” and three amplified single lymphoblastoid cell DNA samples from individual “Family3_Individual4”. The samples names of these 12 are respectively: Family1_Individual1_SingleCell1, Family1_Individual1_SingleCell2, Family1_Individual1_SingleCell3, Family2_Individual2_SingleCell1, Family2_Individual2_SingleCell2, Family2_Individual2_SingleCell3, Family3_Individual3_SingleCell1, Family3_Individual3_SingleCell2, Family3_Individual3_SingleCell3, Family3_Individual4_SingleCell1, Family3_Individual4_SingleCell2, Family3_Individual4_SingleCell3. These 12 amplified single lymphoblastoid cell DNA samples were genotyped using (1) the dynamic model algorithm embedded in the ‘GeneChip Genotyping Analysis Software (GTYPE) version 4.1 (Affymetrix)’ using a homozygous and heterozygous calling threshold of 0.12, (2) the BRLMM algorithm within the ‘Genotyping console 3.0.1’ software (Affymetrix) using a scoring threshold of 0.1 and (3) the Birdseed algorithm of the APT-1.10.1 package (Affymetrix Power Tools) using the ‘birdseed-dev’ command which is the most recently incorporated development version of birdseed from The Broad Institute (http://www.broadinstitute.org/mpg/birdsuite/birdseed.html). The 3 amplified single human blastomere DNA samples were derived from three different human blastomeres that belong to the same in vitro fertilized embryo. This embryo was conceived in vitro by using sperm of person “Family4_father” and an oocyte from person “Family4_mother”. The sample names of these 3 amplified single blastomere DNA samples are respectively: Family4_Blastomere1, Family4_Blastomere2, Family4_Blastomere3. These 3 amplified single human blastomere DNA samples were genotyped using the dynamic model algorithm embedded in the ‘GeneChip Genotyping Analysis Software (GTYPE) version 4.1 (Affymetrix)’ using a homozygous and heterozygous calling threshold of 0.12.

Repositories


GEO

GSE17318

ArrayExpress

E-GEOD-17318

BioProject

PRJNA119043

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Contact


Thierry Voet