|
| Status |
Public on Sep 23, 2021 |
| Title |
EBV transformed lymphoblastoid cell line IB4 |
| Sample type |
genomic |
| |
|
| Source name |
Lymphoblastoid cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IB4
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of genomic DNA from cells was performed using the DNeasy Blood and Tissue Kit from Qiagen (product number 69504).
|
| Label |
cy3,cy5
|
| Label protocol |
200ng of genomic DNA was amplified by at 37°C. using amplification master mix (MSM) and primer/neutralization mix (RPM). After incubation the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).
|
| |
|
| Hybridization protocol |
RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Tecan Freedom Liquid Handling Sytem (Tecan, Maennedorf, Switzerland).
|
| Scan protocol |
After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on iScanner (Illumina).
|
| Description |
Genomic DNA extracted from cell lines was genotyped using Illumina Infinium Omni5-4 v1.1 BeadChip (HumanOmni5-4v1-1_A).
|
| Data processing |
Genomic DNA extracted from cell lines was genotyped using Illumina Infinium Omni5-4 v1.1 BeadChip (HumanOmni5-4v1-1_A).
PLINK was used for data processing
|
| |
|
| Submission date |
Jun 14, 2021 |
| Last update date |
Oct 23, 2023 |
| Contact name |
Matthew Weirauch |
| E-mail(s) |
Matthew.Weirauch@cchmc.org
|
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Center for Autoimmune Genomics and Etiology (CAGE)
|
| Street address |
3333 Burnet Avenue
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45229-3026 |
| Country |
USA |
| |
|
| Platform ID |
GPL30274 |
| Series (2) |
| GSE148396 |
Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci |
| GSE178131 |
Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci [Bead array] |
|
