|
| Status |
Public on Jan 16, 2022 |
| Title |
Ectocervical 3D organoids_with HPV16 E6E7_5days post_Uninfected_Replicate2 |
| Sample type |
RNA |
| |
|
| Source name |
Ectocervical 3D organoids_with HPV16 E6E7_5days post_Uninfected_Replicate2
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: Ectocervical squamous
infection: HPV E6E7
cells culture type: 3D
time: 5days
|
| Treatment protocol |
Ectocervical 2D stem cells and 3D organoids with or with out HPV16 E6E7 expression were either uninfected or infected with Chlamydia trachomatis for 2days and 5days.
|
| Growth protocol |
Ectocervical 2D stem cells and 3D organoids were grown in defined media using the protocol described in the accompanying manuscript (Materials and Methods)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.
|
| Label |
Cy3-CTP
|
| Label protocol |
RNA was labeled with the single-color Low Input Quick Amp Labeling Kit (Agilent Technologies) according to manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
After precipitation, purification and quantification, 0.75µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).
|
| Scan protocol |
Scanning of microarrays was performed with 3µm resolution using a G2565CA high resolution laser microarray scanner (Agilent Technologies).
|
| Data processing |
Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted single-color raw data files were background corrected, quantile normalized, and further analyzed for differential gene expression using Rstudio (Rstudio. Inc.). Microarray data from three independent infection experiments were combined.
|
| |
|
| Submission date |
Apr 20, 2021 |
| Last update date |
Jan 16, 2022 |
| Contact name |
Cindrilla Chumduri |
| E-mail(s) |
cindrilla.chumduri@uni-wuerzburg.de
|
| Organization name |
Julius-Maximilians-Universität Würzburg
|
| Department |
Chair of Microbiology, Biozentrum
|
| Street address |
Am Hubland
|
| City |
Würzburg |
| ZIP/Postal code |
97074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21272 |
| Series (1) |
| GSE172426 |
Gene expression profiles of human patient derived ectocervical stem cells and 3D organoids with and without Chlamydia trachomatis infection |
|
