|
| Status |
Public on Mar 09, 2017 |
| Title |
bEnd3 Gata4 biological rep4 |
| Sample type |
RNA |
| |
|
| Source name |
bEnd3, Gata4
|
| Organism |
Mus musculus |
| Characteristics |
cell type: bEnd3
transduction: Gata4
|
| Treatment protocol |
Conditioned supernatants were harvested 48 h, 60 h and 72 h after transfection, filtered (0.45 μm, Carl Roth) and concentrated using Vivaspin 20 MWCO 100000 columns (Sartorius). Concentrated supernatants were applied to bEnd3 cells. Selection was carried out with 2 μg/ml Puromycin (Invivogen).
|
| Growth protocol |
Synthetic codon optimized cDNA (GeneArt) referring to murine Gata4 (GenBank: AB075549.1) amino acid sequence was cloned in combination with IRES, mCherry, T2A, and puromycin into pLenti-EF1α vector. To obtain mGata4-IRES-mCherry-puromycin and control (IRES-mCherry-puromycin only) expressing lentiviral particles HEK293T cells were co-transfected with vector DNA, pMD2.G L1 (Addgene), pMDLg/pRRE L3 (Addgene), and pRSV rev L2 (Addgene) plasmids using X-tremeGENE 9 (Roche) transfection reagent.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total was RNA from Gata4- or empty vector-transduced bEnd3 cells was extracted with EZNA TM Total-RNA-Kit according to the manufacturer's protocol (OMEGA Biotec).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.
|
| Scan protocol |
Affymetrix GeneArray Scanner3000
|
| Description |
Gene expression data from Gata4-transduced bEnd3
|
| Data processing |
The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary
|
| |
|
| Submission date |
Dec 13, 2016 |
| Last update date |
Mar 09, 2017 |
| Contact name |
Carsten Sticht |
| Organization name |
University Heidelberg
|
| Department |
ZMF
|
| Street address |
Theodor-Kutzer-Ufer
|
| City |
Mannheim |
| ZIP/Postal code |
68169 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22598 |
| Series (2) |
| GSE92356 |
GATA4-dependent organ-specific endothelial differentiation controls liver development and embryonic hematopoiesis (3 of 3) |
| GSE92357 |
GATA4-dependent organ-specific endothelial differentiation controls liver development and embryonic hematopoiesis |
|
