|
| Status |
Public on Mar 22, 2017 |
| Title |
In Vitro HPMCs Treated TGF-β1 and IL-1β Sample 1 vs In Vitro Control HPMCs Sample 1 Replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Omentum-derived HPMC_Treated
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Omentum
|
| Treatment protocol |
To induce MMT in vitro model, omentum-derived HPMC samples were treated with 0.5 ng/ml human recombinant TGF-β1 and 2 ng/ml IL-1β (R&D Systems, Minneapolis, Minnesota, USA) for 72h.
|
| Growth protocol |
HPMCs were cultured in Earle’s M199 medium (Biological Industries, Kibbutz Beit Haemek, Israel) supplemented with 20% fetal bovine serum (FBS; Thermo Scientific, Cramligton, UK), 50 U/ml penicillin, 50 µg/ml streptomycin (PPA Laboratories GmbH, Pasching, Austria), 2% Biogro-2 (Biological Industries).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Tri-Reagent following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
400-800 ng of total RNA was labeled using Quick Amp Labeling Kit, two-color (Agilent Technologies) following manufacturer's instructions.
|
| |
|
| Channel 2 |
| Source name |
Omentum-derived HPMC_Control
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Omentum
|
| Treatment protocol |
To induce MMT in vitro model, omentum-derived HPMC samples were treated with 0.5 ng/ml human recombinant TGF-β1 and 2 ng/ml IL-1β (R&D Systems, Minneapolis, Minnesota, USA) for 72h.
|
| Growth protocol |
HPMCs were cultured in Earle’s M199 medium (Biological Industries, Kibbutz Beit Haemek, Israel) supplemented with 20% fetal bovine serum (FBS; Thermo Scientific, Cramligton, UK), 50 U/ml penicillin, 50 µg/ml streptomycin (PPA Laboratories GmbH, Pasching, Austria), 2% Biogro-2 (Biological Industries).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Tri-Reagent following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
400-800 ng of total RNA was labeled using Quick Amp Labeling Kit, two-color (Agilent Technologies) following manufacturer's instructions.
|
| |
|
| |
| Hybridization protocol |
Whole Human Genome Microarray Kit, 4x44K (Agilent Technologies) was used in hybridations. Controls and samples were incubated in blocking agent and fragmentacion buffer. Labeled RNA was added in incubation buffer and applied to microarray. Excess fluorochrome and unhybridized RNA was eliminated with different stringencies saline buffer. Stabilization solution and dry recomended by Agilent Technologies was employed.
|
| Scan protocol |
Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction v9.5 Software.
|
| Data processing |
Babelomics free software (babelomics.bioinfo.cipf.es) was used for background subtraction and LOESS/ LOWESS and quantiles normalization.
|
| |
|
| Submission date |
Dec 15, 2016 |
| Last update date |
Mar 22, 2017 |
| Contact name |
Vicente Ruiz-Carpio |
| Organization name |
Centro de Biología Molecular "Severo Ochoa"
|
| Department |
Biología Celular e Inmunologia
|
| Lab |
406
|
| Street address |
Nicolás Cabrera, 1
|
| City |
Madrid |
| ZIP/Postal code |
28049 |
| Country |
Spain |
| |
|
| Platform ID |
GPL6848 |
| Series (2) |
| GSE92454 |
Mesenchymal Transition in Human Mesothelial Cells In Vitro and Ex Vivo [TGF-β1 and IL-1β treatment] |
| GSE92455 |
Mesenchymal Transition in Human Mesothelial Cells In Vitro and Ex Vivo |
|
