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Status |
Public on Aug 05, 2014 |
Title |
Genotyping of iPS 19 11. UW, Stamlab (NREMC); iPS DF 19.11 Cell Line, Induced pluripotent stem cell; JS-DE19.11-genotype |
Sample type |
genomic |
|
|
Source name |
iPS DF 19.11 Cell Line, Induced pluripotent stem cel, derived from fibroblast. the first set of numbers before the period refer to different clones, the number after the period indicates the sub-clone.; JS-DE19.11-genotype
|
Organism |
Homo sapiens |
Characteristics |
disease: None biomaterial_provider: James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison biomaterial_type: Cell Line line: iPS DF 19.11 Cell Line lineage: Derived from newborn foreskin fibroblast: Cat# CRL-2097TM, ATCC differentiation_stage: Induced pluripotent stem cell differentiation_method: http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1 passage: 31 medium: NA Sex: Unknown batch: NA
|
Treatment protocol |
None
|
Growth protocol |
http://roadmapepigenomics.org/protocols
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Qiagen DNeasy Blood and Tissue kit (cat #69506).
|
Label |
Illumina protocol
|
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.
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Hybridization 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
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Description |
sample_term_id: NTR_0001173 assay_term_id: OBI_0001393 nucleic_acid_term_id: SO_0000352 Genotyping EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.19794 sample alias: iPS_19_11 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5333
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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.
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Submission date |
Jul 31, 2014 |
Last update date |
Jan 29, 2015 |
Contact name |
Northwest REMC |
E-mail(s) |
rharris1@bcm.tmc.edu
|
Organization name |
University of Washington
|
Street address |
-
|
City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98195 |
Country |
USA |
|
|
Platform ID |
GPL18952 |
Series (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
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Relations |
BioSample |
SAMN00204008 |