|
| Status |
Public on Feb 13, 2019 |
| Title |
1_P2 |
| Sample type |
RNA |
| |
|
| Source name |
human bioprinted liver RNA
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: MTX
concentration: 0.209
-/+ kcs: Yes
time: Tx28
print: Print 2
|
| Treatment protocol |
Treatment was initiated on Day 7 post-manufacture. Dosing medium was replaced every 24hrs. Two treatment regimens were used for each tissue composition in which tissues were continuously exposed for either 14 or 28 days.
|
| Growth protocol |
3D bioprinted tissues were manufactured using previously described methods (Norona et al., 2016). Tissues were allowed to mature for 6 days post-manufacture before initiating studies.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue lysates were prepared for each treatment group by homogenization in TRIzol® Reagent (ThermoFisher Scientific, Waltham, MA) using PreCellys RNase-free microfuge tubes and the Precellys 24 homogenizing instrument (Bertin Corp., Rockville, MD). Total RNA was isolated using the Direct-Zol™ RNA MiniPrep kit per the manufacturer’s instructions (Zymo Research, Irvine, CA).
|
| Label |
biotin
|
| Label protocol |
Double-stranded cDNA was synthesized from 50-150 ng (dependent on RNA yield) of total RNA, then transcribed to biotin-labeled cRNA using the 3’ Express IVT kit (Affymetrix) according to manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
Labeled cRNA (15 μg) was fragmented and prepared for hybridization
|
| Scan protocol |
The Affymetrix Clariom S Human 96 peg arrays were used with the Affymetrix Gene Titan system. Gene Titan robotic instrumentation was used to perform the hybridization, washing, and scanning of the peg arrays.
|
| 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. Samples > 3 SD away from the mean suggest these samples may be aberrant and were therefore omitted from analysis (3_P3, 1_P3, 20_P1 and 14_P3). A filtering step was performed to remove control probe sets and the mean + 1 SD of the antigenomic probe sets was used to filter low expression probe sets. Gene expression differences were identified using ANOVA models with linear contrasts.
|
| |
|
| Submission date |
Apr 25, 2018 |
| Last update date |
Feb 13, 2019 |
| Contact name |
Leah M. Norona |
| E-mail(s) |
[email protected]
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Institute for Drug Safety Sciences
|
| Street address |
6 Davis Drive
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL24324 |
| Series (1) |
| GSE113630 |
Gene expression data from bioprinted liver tissues treated with 0.1% DMSO (dimethyl sulfoxide: vehicle), 10 ng/mL transforming growth factor beta 1 (TGF-β1) or 0.209 µM methotrexate (MTX) for either 14 or 28 days. |
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