Comment[GEAAccession]	E-GEAD-283
MAGE-TAB Version	1.1
Investigation Title	Generation of human leukocyte antigen-homozygous human induced pluripotent stem cells
Experiment Description	Homologous recombination is an efficient tool of genome engineering. We applied the chromosome crossing-over(CO) event according to the homologous recombination for generating intentional HLA region homogenization. The combination of allele-specific double strand breaks by CRISPR/Cas9 and suppression of transcripts or proteins derived from the Bloom syndrome (BLM) gene is required for such generation. In this study, our phenotype of interest is recombination induced by CRISPR/Cas9 under the reduction of BLM repression. Using genotypes of SNP markers, we found extensive individual variation in the number of recombination events in the hiPS cells. To detect CO events in hiPSCs, we used Infinium Omni5-4 BeadChip for the analysis of the SNPs copy number of hiPSC-BLM+/+, hiPSC-BLMtet/tet, AAVS1 cNP/+,  hiPSC-BLMtet/tet;AAVS1 cNP/+, DOX(+)9M CRISPR(+), hiPSC-BLMtet/tet;AAVS1 cNP/+;DOX(-), ML216 (+)9M CRISPR(+),hiPSC-BLM+/+;ML(216), and HLAI-III-CRISPR(+). Data were analyzed using the Illumina GenomeStudio.
Experimental Design	genotype design	genotyping design	array specific design
Experimental Factor Name	genetic_modification
Experimental Factor Type	genetic_modification
Person Last Name	yoshimura
Person First Name	yasuhide
Person Affiliation	Division of Gene Therapy Science, Department of Genome Biology, Graduate School of Medicine, Osaka University
Person Roles	submitter
Public Release Date	2022-09-04
Protocol Name	P-GEAD-23	P-GEAD-24	P-GEAD-25	P-GEAD-26	P-GEAD-27	P-GEAD-28
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol	normalization data transformation protocol
Protocol Description	genomic DNA was isolated from iPS cells	as per QIAGEN protocol	as per illumina  protocol	as per illumina  protocol	as per illumina  protocol	as per illumina  protocol
SDRF File	E-GEAD-283.sdrf.txt
Comment[Number of channel]	dual-channel
Comment[Array Design REF]	A-GEAD-2
Comment[AEExperimentType]	genotyping by array
Comment[BioProject]	PRJDB7397
Comment[Last Update Date]	2022-09-04