|
| Status |
Public on Sep 16, 2017 |
| Title |
Endothelin-1 + Verapamil_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
iCell® Cardiomyocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: derived cardiomyocytes from hiPSC
treatment: 10 nM Endothelin-1 + 1 uM Verapamil
|
| Treatment protocol |
The cardiomyocytes were untreated or treated with endothelin-1 in the presence of either vehicle (DMSO), Ivermectin, Importazole, IPA-3, or verapamil for 18 hours.
|
| Growth protocol |
iCell® Cardiomyocytes (Cellular Dynamics International) were maintained in Maintenance Medium (Cellular Dynamics International).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using QIAzol Lysis Reagent (Qiagen).
Whole transcriptome barcoded cDNA library is first generated with SuperScript® VILO™ cDNA Synthesis kit (Thermo Fisher Scientific) from 20 ng of total RNA. Then cDNA is amplified using Ion AmpliSeq™ technology to accurately maintain expression levels of all targeted genes. Amplified cDNA Libraries were evaluated for quality and quantified using Ion Library TaqMan Quantitation Kit (Thermo Fisher Scientific). Libraries were then diluted to 75 pM and pooled equally, with fourteen individual samples per pool.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Base calling was performed using software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.0.4).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
RPM were calculated using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
Genome_build: hg19_AmpliSeq_Transcriptome_ERCC_v1
Supplementary_files_format_and_content: *txt: Tab-delimited text files include gene symbol and gene expression (RPM) for each sample.
|
| |
|
| Submission date |
Mar 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yoshiyuki Tsujihata |
| E-mail(s) |
yoshiyuki.tsujihata@takeda.com
|
| Phone |
+81-466-32-1788
|
| Organization name |
Takeda Pharmaceutical Company Limited
|
| Street address |
26-1, Muraoka-Higashi 2-chome
|
| City |
Fujisawa |
| State/province |
Kanagawa |
| ZIP/Postal code |
2518555 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17303 |
| Series (2) |
| GSE96987 |
AmpliSeq analysis of human iPSC-derived cardiomyocytes |
| GSE96989 |
RNA sequencing analysis of cardiomyocytes |
|
| Relations |
| BioSample |
SAMN06639905 |
| SRA |
SRX2670629 |
