|
| Status |
Public on Dec 31, 2019 |
| Title |
THP-1_E_Control HDE |
| Sample type |
RNA |
| |
|
| Source name |
THP-1 monocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1
hepatocyte donor id: E
treatment: Control HDE
|
| Treatment protocol |
Exposures were conducted in 96-well round-bottom plates (Corning) at a density of 1 x 10^5 cells per well. THP-1 monocytes were exposed to 200 µg/ml HDE or the matched volume of mock in separate experiments for each hepatocyte donor.
|
| Growth protocol |
THP-1 human monocytes (TIB-202, ATCC) were cultured in suspension in RPMI-1640 (ATCC) supplemented with 10% (v/v) Exosome-Depleted FBS (Gibco), penicillin-streptomycin (Gibco), and 0.05 mM β-mercaptoethanol (Sigma).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in QIAzol (Qiagen) and isolated using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Following purification, 5.5 µg of ss-cDNA were fragmented and end labeled with biotin before hybridizing to the array plate
|
| |
|
| Hybridization protocol |
GeneTitan robotic instrumentation was used to perform the hybridization, washing, and scanning of the peg array using the Affymetrix GeneTitan Hybridization, Wash, and Stain Kit for WT Arrays.
|
| Scan protocol |
GeneTitan robotic instrumentation was used to perform the hybridization, washing, and scanning of the peg array using the Affymetrix GeneTitan Hybridization, Wash, and Stain Kit for WT Arrays.
|
| Description |
THP-1 RNA
|
| Data processing |
Affymetrix CEL files were normalized using Robust Multi-array Average (RMA) method with a log base 2 (log2) transformation (Irizarry et al., 2003). Principal component analysis (PCA) was used to evaluate the overall performance of the arrays and identify outliers. A filtering step was performed to remove low expression probe sets. Gene expression differences were identified using ANOVA models with linear contrasts.
|
| |
|
| Submission date |
Jan 25, 2019 |
| Last update date |
Jan 01, 2020 |
| Contact name |
Merrie Mosedale |
| Organization name |
UNC Eshelman School of Pharmacy
|
| Department |
Division of Pharmacotherapy and Experimental Therapeutics
|
| Lab |
Institute for Drug Safety Sciences
|
| Street address |
301 Pharmacy Lane, Kerr Hall CB#7569
|
| City |
Chapel Hill |
| State/province |
North Carolina |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL24324 |
| Series (1) |
| GSE125690 |
Gene expression data from THP-1 cells exposed to exosomes from acetaminophen-treated or vehicle-treated hepatocytes or corresponding mock- or medium-controls |
|
