|
| Status |
Public on Mar 27, 2020 |
| Title |
MP-69 |
| Sample type |
genomic |
| |
|
| Source name |
liver hepatocytes
|
| Organism |
Homo sapiens |
| Characteristics |
ancestry: 0.8555
gender: Female
age: 28
batch: batch_2_2017
sentrix_id: 201332610023
sentrix_position: R06C01
|
| Treatment protocol |
N/A
|
| Growth protocol |
Cells were plated at a density of 0.6 x 106 cells/well in 500 µL InVitroGro-CP media (BioIVT, Baltimore, MD) in collagen-coated plates with matrigel (Corning, Bedford, MA) overlay and incubated overnight at 37° C. Cultures were maintained in InVitroGro-HI media (BioIVT) supplemented with Torpedo antibiotic mix (BioIVT) per the manufacturer's instructions. The media was replaced every 24 hours for three days. For primary hepatocyte cultures, cell viability was determined by trypan blue (Lonza) exclusion using a hemocytometer (Fisher Scientific).78 If viability was low, Percoll gradient (Sigma-Aldrich) centrifugation of cell suspensions was carried out to improve the yield of viable cells. Cell were plated at a density of 0.6 × 106 cells/well in 500 µL InVitroGro-CP media (BioIVT, Baltimore, MD) in collagen-coated plates with matrigel (Corning, Bedford, MA) overlay and incubated overnight at 37 °C. Cultures were maintained in InVitroGro-HI media (BioIVT) supplemented with Torpedo antibiotic mix (BioIVT) per the manufacturer’s instructions. The media was replaced every 24 h for 3 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from each hepatocyte line using Gentra Puregene Blood kit (Qiagen).
|
| Label |
Cy3, Cy5
|
| Label protocol |
SNPs were genotyped using Illumina Multi-Ethnic Genotyping array (MEGA) at the University of Chicago Functional Genomics Core using standard protocols.
|
| |
|
| Hybridization protocol |
Samples were processed for array hybridization using Illumina provided array reagents.
|
| Scan protocol |
Standard protocol.
|
| Description |
novel eQTLs in African-Americans
|
| Data processing |
Genotyping outputs were created by Genome Studio using 0.15 GenCall score cutoff.
|
| |
|
| Submission date |
Mar 27, 2020 |
| Last update date |
May 06, 2022 |
| Contact name |
Minoli Perera |
| E-mail(s) |
minoli.perera@northwestern.edu
|
| Organization name |
Northwestern Univeristy
|
| Department |
Pharmacology
|
| Street address |
303 E Chicago Ave.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60608 |
| Country |
USA |
| |
|
| Platform ID |
GPL24127 |
| Series (2) |
| GSE124076 |
Uncovering the role admixture in health disparities: Association of hepatocyte gene expression and DNA methylation to African Ancestry in African-Americans |
| GSE147628 |
African American hepatocyte genotype |
|
