|
| Status |
Public on Sep 14, 2022 |
| Title |
T16; Untreated rep1 |
| Sample type |
RNA |
| |
|
| Source name |
AC16 cells human ventricular cardiomyocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell line/type: AC16 human ventricular cardiomyocytes
treatment/time point: collected 16 hours (T16) after synchronization
|
| Treatment protocol |
Digoxin 0.5µM or 5µM
|
| Growth protocol |
The AC16 human cardiomyocyte cell line was obtained from Millipore (SCC109). Cells were maintained in DMEM/F12 Ham (Sigma-Aldrich) supplemented with 2mM L-Glutamine (Thermo Fisher Scientific), 12.5% of fetal bovine serum (FBS) and 1% penicillin-streptomycin (Thermo Fisher Scientific).Cells were synchronized with 100nM dexamethasone for 2h followed by PBX washes. Cells were treated with digoxin (0.5 or 5µM) and cells were lysed 4, 16 and 20 hours after the treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction from cultured cells was carried out using the NucleoSpin® RNA Midi kit according to the manufacturer’s instruction (Macherey-Nagel).
|
| Label |
biotin
|
| Label protocol |
Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 5,5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip Human Transcriptome Array 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using GeneChip Scanner GCS3000.
|
| Description |
Samples from untreated AC16 cells collected 16 hours (T16) after synchronization
13_T16_rep1
|
| Data processing |
Raw data were processed further using GIANT (Galaxy-based interactive tools for Analysis of Transcriptomic data). This user-friendly tool suite was developed in-house for microarray and RNA-seq differential data analysis. It consists of modules allowing to perform quality control (QC), Robust Multi-Average method normalization, LIMMA differential analysis, volcano plot and heatmaps.
|
| |
|
| Submission date |
Sep 08, 2021 |
| Last update date |
Sep 14, 2022 |
| Contact name |
Philippe Lefebvre |
| E-mail(s) |
[email protected]
|
| Organization name |
INSERM UMR 1011, Université Lille-Nord de France
|
| Street address |
Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc
|
| City |
Lille |
| ZIP/Postal code |
59045 |
| Country |
France |
| |
|
| Platform ID |
GPL19251 |
| Series (2) |
| GSE183659 |
Transcriptomic analysis of synchonized AC16 cells treated with 0.5µM or 5µM digoxin after T0, T4, T16 and T20. |
| GSE183661 |
Vehicle or Digoxin treatment in AC16 cells and mouse |
|
