|
| Status |
Public on Jul 27, 2022 |
| Title |
7013-100pg |
| Sample type |
genomic |
| |
|
| Source name |
UTAH/CEPH cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: UTAH/CEPH
cell type: lymphoblastoid cell lines
dna amount: 100pg DNA sample
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extraction protocol not provided.
|
| Label |
cy3, cy5
|
| Label protocol |
The DNA samples were denatured and neutralized before adding the Amplification Master Mix. The amplification plate was incubated in a 37°C hybridization oven for approximately 23 hours. Samples were then split in half for subsequent processing, with both halves receiving the same treatment. Enzymatic fragmentation was carried out by adding FRG to each sample and incubating the plate at 37°C for one hour. The DNA was precipitated out using PA1 and 100% 2-propanol, which resulted in a blue pellet in the bottom of each well. Reagent RA1 was added to each sample to resuspend the precipitated DNA.
|
| |
|
| Hybridization protocol |
Following resuspension, the samples were combined back into their original wells, and 70µL was loaded onto the Omni5 beadchips (four samples per chip). Hybridization of the samples to the beadchips was carried out in a 48°C hybridization oven for about 24 hours. Beadchips were washed to prepare for the staining process and assembled into Flow-Through Chambers using LCG glass and LCG spacers.
|
| Scan protocol |
Flow-Through Chambers were placed into the Chamber Rack of a 44°C water circulator where RA1 reagent was used to wash away unhybridized DNA. Extension and staining (XStain) were performed on each beadchip: the surface of the beadchips was conditioned for the extension reaction, primer extension was performed using labeled nucleotides, hybridized DNA was removed using 95% formamide/1mM EDTA, and the labeled extended primers underwent a multi-layer staining process. The stained beadchips were washed and coated, and then dried in a vacuum desiccator for approximately one hour before imaging on the Illumina iScan.
|
| Description |
100pg.vcf
|
| Data processing |
Initial data screening, including assessment of Illumina’s internal controls, was performed using GenomeStudio 2.0.5 software.
Processed data contains: Genotype: AA,AB,BB,or NC (no call)
|
| |
|
| Submission date |
Jul 26, 2022 |
| Last update date |
Jul 27, 2022 |
| Contact name |
Jianye Ge |
| E-mail(s) |
jianye.ge@unthsc.edu
|
| Organization name |
University of North Texas Health Science Center
|
| Department |
Center for Human Identification
|
| Street address |
3500 Camp Bowie Blvd
|
| City |
Fort Worth |
| State/province |
TX |
| ZIP/Postal code |
76107 |
| Country |
USA |
| |
|
| Platform ID |
GPL30274 |
| Series (1) |
| GSE209804 |
A robust machine learning approach for missing persons cases with high genotyping errors |
|
