|
| Status |
Public on Sep 01, 2019 |
| Title |
H6 |
| Sample type |
RNA |
| |
|
| Source name |
Ectocervical squamous_Wnt-deficient media_EarlyOrganoids_hc036
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: Ectocervical squamous
media: Wnt-deficient media
organoid type: EarlyOrganoids
patient-id: hc036
passage: P1
|
| Treatment protocol |
Cells were cultured in 2D (without feeders) or 3D Matrigel cultures in the described media. Differentiated organoids were harvested at 2 weeks after seeding while early organoids were harvested at 3 days post seeding into matrigel.
|
| Growth protocol |
Ecto- and endocervical cells were grown in corresponding media as described in the accompanying publication (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.10.10.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted single-color raw data txt files were further analyzed using R and the associated BioConductor package limma. Background was removed using method normexp with offset 15, followed by quantile normalization.
|
| |
|
| Submission date |
Sep 19, 2016 |
| Last update date |
Sep 01, 2019 |
| Contact name |
Thomas F Meyer |
| E-mail(s) |
tfm@mpiib-berlin.mpg.de
|
| Phone |
03028 460 404
|
| Organization name |
Max Planck Institute for Infection Biology
|
| Department |
Molecular Biology
|
| Street address |
Chariteplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21272 |
| Series (2) |
| GSE87074 |
Gene expression profiles of human cervical primary cells from ecto- and endocervix |
| GSE87076 |
Gene expression profiles of cultured stem cells and organoids from the uterine cervix of human and mouse |
|
