|
| Status |
Public on Aug 05, 2014 |
| Title |
Genotyping of H1. UW, Stamlab (NREMC). H1 cell line; JS-ESCH1-genotype |
| Sample type |
genomic |
| |
|
| Source name |
Human embryonic stem cells received from the James Thompson laboratory. Cells are from the H1 line.; JS-ESCH1-genotype
|
| Organism |
Homo sapiens |
| Characteristics |
disease: None
biomaterial_provider: James Thompson Laboratory
biomaterial_type: Cell Line
line: H1
lineage: Embryonic Stem Cell
differentiation_stage: None
differentiation_method: None
passage: Between 20 and 40
medium: mTeSER
Sex: Male
batch: H1U
|
| 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.
|
| |
|
| 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
|
| Description |
sample_term_id: EFO_0003042
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.19800
sample alias: H1-13
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3425
|
| 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.
|
| |
|
| 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 |
|
| Relations |
| BioSample |
SAMN00114950 |
