alias: JS-ESCH1-genotype
center_name: NREMC

STUDY_REF: UwStam_NREMC_CA
SAMPLE_DESCRIPTOR: SRS116483

ATTRIBUTES
EXPERIMENT_TYPE: Genotyping Array
PLATFORM: GPL16104
GROWTH_PROTOCOL: http://roadmapepigenomics.org/protocols
TREATMENT_PROTOCOL: None
EXTRACT_PROTOCOL: Qiagen DNeasy Blood and Tissue kit (cat #69506).
LABEL_PROTOCOL: The chip underwent staining and extension in capillary flow-through chambers. Allele-specific single-base extension of the oligos on the beadchip, using the captured DNA as template, incorporated detectable labels on the beadchip and determined the genotype call for the sample.
HYB_PROTOCOL: 200ng of genomic DNA was first denatured and subsequently neutralized to prepare it for amplification. The denatured DNA was then isothermally amplified in an overnight step at 37°C. Next, amplified DNA was enzymatically fragmented for 60 minutes at 37°C using an end-point fragmentation process. The fragmented DNA was then precipitated with isopropanol, allowed to air dry, then resuspended in hybridization buffer. Eight samples were subsequently applied to each HumanOmni2.5-8v1.1 beadchip, which were kept separate with an IntelliHyb seal. The prepared beadchip was incubated overnight in a hybridization oven at 48°C for 16-24 hours with rocking. The amplified and fragmented DNA samples annealed to locus-specific 50mers during hybridization. Following hybridization, unhybridized and non-specifically hybridized DNA was washed away, and the chip was prepared for staining and extension.
SCAN_PROTOCOL: Beadchips were scanned using an Illumina iScan+ with ICS v3.2.28
DATA_PROCESSING: Intensity data was extracted with Illumina GenomeStudio software (GenomeStudio v2011.1 with Genotyping Module v1.9.4) with a GenCall cutoff of 0.15.
PROBE_GROUP_FILE: Illumina HumanOmni2.5-8v1.1 beadchip
META-PROBESET_FILE: None
VALUE_DEFINITION: None