|
| Status |
Public on Apr 01, 2022 |
| Title |
Orange 1 |
| Sample type |
RNA |
| |
|
| Source name |
cell treated with Orange cells (BT-OC)
|
| Organism |
Homo sapiens |
| Characteristics |
tag: hair follicle dermal papilla cells
|
| Treatment protocol |
After the initial 24 hour seeding in 6-well-collagen-coated plates. The medium was changed with 0 (Control) and 1:2000 Orange cells (BT-OC) for 48 h.
|
| Growth protocol |
HFDPCs were purchaced from Cell application and were maintained in Papilla cell culture meduim
|
| 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 APC 50% for 48 h
|
| 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 top DEGs.
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files ).
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| |
|
| Submission date |
Mar 29, 2022 |
| Last update date |
Apr 02, 2022 |
| Contact name |
Meriem Bejaoui |
| E-mail(s) |
mariembejaoui.mb@gmail.com
|
| Organization name |
University of Tsukuba
|
| Street address |
1 Chome-1-1 Tennodai
|
| City |
Tsukuba, |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8577 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13667 |
| Series (1) |
| GSE199651 |
Expression data from Orange cells (BT-OC) -treated HFDPCs |
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