|
| Status |
Public on Dec 08, 2021 |
| Title |
hiPSC-CM control A1 |
| Sample type |
SRA |
| |
|
| Source name |
Induced Pluripotent Stem Cell derived cardiomyocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: iCell cardiomyocytes (Cellular Dynamics)
treatment: EtOH 0.01% for 24 hours
|
| Treatment protocol |
The day before treatment, the cells were fed with serum-free (BMCC) medium. The specific culture media were completely replaced with fresh media prior to compound addition and after four hours of stabilization at 5% CO2 and at 37 °C, cells were treated by adding a 1:10 dilution of each 10x compound working solutions. The final compound concentrations used were 0.01% EtOH and 1 nM T3. Total RNA was extracted 24h after treatments.
|
| Growth protocol |
The cardiomyocytes were thawed in iCell Cardiomyocytes Plating Medium and directly plated onto fibronectin-coated CytoView MEA 48 wells white plates (Axion Biosystem, Atlanta, GA, USA) at 3x104 plated viable cells per well, based on lot specific plating efficiency. The hiPSC-CMs were incubated at 37 °C with 5% CO2 and allowed to attach for 2 h in moisturized conditions, prior filling each well with 0.3 mL of Plating medium. On day 2 post-plating, the spent medium was replaced with iCell Maintenance (iCM) medium and thereafter 50% of the medium was replaced every 2-3 days, up to cells treatment. Before the experiments, hiPSC-CMs were cultured for four weeks after plating to improve their functional maturation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using total RNA mini kit (Norgen Biotech Corp.) following manufacturer’s instructions.
RNA libraries were prepared Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (following Ion Torrent user guide, Publication Number MAN0010742 ); for sequencing was usde Ion 540™ Kit – Chef (following Ion Torrent user guide, Publication Number MAN0010851)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent S5 |
| |
|
| Description |
Sample A1
Data_Matrix_AvsB.xlsx
Filtered_Normalized_Data_AvsB.xlsx
Differential_Expression_AvsB.xlsx
GO_BP_Functional_Analysis_AvsB.xlsx
|
| Data processing |
The reads were mapped and analyzed with the Torrent Suite (version 5.12.1). AmpliseqRNA plugin (version 5.12.0.1) was used to map the sequencing reads on Target Regions.
Reference Library: hg19_ampliseq_transcriptome_ercc_v1(hg19 AmpliSeq Transcriptome ERCC v1)
Target Regions: hg19_AmpliSeq_Transcriptome_21K_v1.bed
Genome_build: hg19 AmpliSeq Transcriptome ERCC v1
Normalization method CPM (counts per million): counts scaled by total number of reads
The differential analysis was carried out with the R package edgeR
Supplementary_files_format_and_content: Data matrix
Supplementary_files_format_and_content: Filtered Normalized Data
Supplementary_files_format_and_content: Differential Expression
Supplementary_files_format_and_content: GO.BP functional analysis
|
| |
|
| Submission date |
Apr 19, 2021 |
| Last update date |
Dec 08, 2021 |
| Contact name |
Alessandra Ulivieri |
| Organization name |
Niccolò Cusano University Foundation
|
| Department |
Laboratory of Biomedical Research
|
| Street address |
Via Don Carlo Gnocchi 3
|
| City |
Rome |
| ZIP/Postal code |
00166 |
| Country |
Italy |
| |
|
| Platform ID |
GPL23934 |
| Series (1) |
| GSE172348 |
Thyroid Hormone effects on hiPSC-derived cardiomyocytes (hiPSC-CM). Identification of target genes and pathways by RNA-Seq analysis |
|
| Relations |
| BioSample |
SAMN18796895 |
| SRA |
SRX10636230 |
