|
| Status |
Public on Jan 08, 2021 |
| Title |
HEK239flpGR_siNON_vehicle_6h_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Isogenic HEK293 cells, wild-type GR, siNON treated, 72h, vehicle treated, 6h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
cell type: human embryonal kidney cell line
stably expressing: wild-type GR
sirna treatment: Dharmacon On-TARGETplus SMARTpool for nontargeting pool
sirna concentration: 40 nM
time for sirna: 72 h
ligand treatment: EtOH vehicle
ligand concentration: 0.01%
time for ligand: 6 h
|
| Treatment protocol |
siUBC9 or siNON in 40 nM final concentration were added with Lipofectamine RNAiMAX to 6-well plates and incubated for 20 min RT. Subsequently, 300,000 isogenic HEK293 cells were seeded at each 6-well plates and allowed to grow in steroid-depleted medium (2.5% charcoal stripped FBS in DMEM) 72 h. The cells were treated with or without 100 nM of dexamethasone for 6 h prior extraction of RNA.
|
| Growth protocol |
Isogenic HEK293 cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, and 100 µg hygromycin-B, and kept at 37 °C in a humidified 95% air/ 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TriPure (Roche Diagnostics GmbH, Mannheim, Germany) according to manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmk kit for Illumina arrays.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol.
|
| Scan protocol |
Standard Illumina scanning protocol. Arrays were scanned by Illumina BeadArray Reader.
|
| Description |
NON_2
HEK293flpGR cells were created by using the Flp-In System (Invitrogen).
|
| Data processing |
Obtained data was normalized using VST transformation and RSN normalization used as standard approach for Illumina arrays with the R/lumi package.
|
| |
|
| Submission date |
Dec 19, 2014 |
| Last update date |
Jan 08, 2021 |
| Contact name |
Ville Paakinaho |
| E-mail(s) |
villepaakinaho@gmail.com
|
| Organization name |
University of Eastern Finland
|
| Department |
School of Medicine
|
| Lab |
Biomedicine
|
| Street address |
Yliopistonranta 8
|
| City |
Kuopio |
| ZIP/Postal code |
70210 |
| Country |
Finland |
| |
|
| Platform ID |
GPL10558 |
| Series (2) |
| GSE64372 |
SUMOylation regulates the protein network and chromatin accessibility at glucocorticoid receptor-binding sites [array] |
| GSE64373 |
SUMOylation regulates the protein network and chromatin accessibility at glucocorticoid receptor-binding sites |
|
