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| Status |
Public on Mar 11, 2016 |
| Title |
ESC derived EBs after 18h of differentiation in the presence of 1.88µM GSK-J4 (KDM6 specific inhibitor) in EB medium |
| Sample type |
RNA |
| |
|
| Source name |
inhibitor-treated ESC derived EBs from R1 background
|
| Organism |
Mus musculus |
| Characteristics |
treatment: 18h of differentiation in the presence of 1.88µM GSK-J4 (KDM6 specific inhibitor) in EB medium
cell line: R1 mouse ESC line
|
| Treatment protocol |
For harvest, EBs were transferred to 15 ml Falcon tubes and allowed to sediment. Medium was replaced by Trypsin/EDTA followed by 3 min incuation at 37°C. Dissociation of EBs was done by pipetting up and down.
|
| Growth protocol |
For ESC differentiation, feeder-depleted ESC (separation via 0.1% gelatin-coated plates, incubated for 45 min at 37°C) were cultured in ESC medium with LIF-withdrawal in bacteriological Petri dishes and incuated for 18h in a 37°C, 5% CO2 incubator in the presence of EB medium only, DMSO, GSK-J5 or GSK-J4 (both 1,88 µM).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
100ng of total RNA were amplified with the WT Expression Kit (Ambion), followed by ssDNA labeling with the WT Terminal Labeling Kit (Affymetrix); all steps were performed according to the manufacturers' protocols.
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| |
|
| Hybridization protocol |
130µl hybridization mix prepared from labeled ssDNA was hybridized for 17h at 45°C to GeneChip Mouse Gene 2.0 ST arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_002.
|
| Scan protocol |
Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
Gene expression data from ESC derived EBs of 18h of differentiation in the presence of GSK-J4
|
| Data processing |
Data were preprocessed with the Expression Console v1.2.1.20 software (Affymetrix); background correction, nomalization and gene-level probeset summary were performed with the RMA sketch workflow using default parameter settings.
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| |
|
| Submission date |
Aug 14, 2013 |
| Last update date |
Mar 12, 2016 |
| Contact name |
Claus Juergen Scholz |
| Organization name |
University Hospital Würzburg
|
| Department |
Core Unit SysMed
|
| Street address |
Josef-Schneider-Str. 2
|
| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE49886 |
KDM6 Inhibition induces DNA Damage Response (DDR) during ESC Differentiation but not during self-renewal. |
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