|
| Status |
Public on Nov 11, 2021 |
| Title |
hAECs+ EEA 3 |
| Sample type |
RNA |
| |
|
| Source name |
amnion epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: EEA for 7 days
|
| Treatment protocol |
After the initial 24 hour culture, the medium was changed with EEA (at the concentration of 20 µg/ml ) every 48 hours for three times (7days) for the treatment samples. Control samples were maintained in Placental medium that was also changed every 48 hours. Finally, we collected the treatment and control samples from one-week culture.
|
| Growth protocol |
AECs were isolated from delivered term placenta and were maintained in Placenta Epithelial Cell Basal Medium (PromoCell, Cat. # C-26140) in 2D culture plate. Finally, 3D spheroids were formed by seeding 1×106 AECs in Placenta Basal Epithelial Cell Medium into each well of the 24-well plate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added and the cell suspensions were centrifuged for 5 minutes at 500 g and the pellet was stored at -80oC until use.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA
|
| |
|
| Hybridization protocol |
Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HG-219). GeneChips were washed and stained in the Gene Atlas Fluidics Station 400
|
| Scan protocol |
GeneChips were scanned using the GeneAtlas Imaging Station
|
| Description |
Gene expression data from EEA treated hAECs on 7th day
|
| Data processing |
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) for the DEGs between day 7 treated hAECs and D0 hAECs and for DEGs between day 7 treated hAECs and D7 hAECs to test whether a priori-defined groups of genes associated with neural differentiation were significantly related to the DEGs between EEA-treated and control cells on day 0 and day 7
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| |
|
| Submission date |
Nov 08, 2021 |
| Last update date |
Nov 12, 2021 |
| Contact name |
Farhana Ferdousi |
| E-mail(s) |
farhana_ferdousi24@yahoo.com
|
| Organization name |
University of Tsukuba
|
| Street address |
1-1-1 Tennodai
|
| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8572 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13667 |
| Series (1) |
| GSE188411 |
Expression data from ethanol extract of Aurantiochytrium Sp. (EEA)-treated human amnion epithelial cells (hAECs) |
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