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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 24, 2017 |
| Title |
Plate D1; Treatment Camptothecin |
| Sample type |
SRA |
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| Source name |
iPS-derived cardiomyocytes_Camptothecin
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| Organism |
Homo sapiens |
| Characteristics |
cell type: iPS-derived cardiomyocytes
plate: D1
compound name: Camptothecin
time point: after 12h of compound treatment
barcode id: IonXpress_045
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| Treatment protocol |
To screen for drugs that prevent development of the diabetic phenotype, an 80-compound subset of the Screen-well ICCB Known Bioactives library (Enzo life sciences) was used. For each 96-well plate: vehicle control (DMSO); GEC negative control (glucose 1 mM, ET-1 5 nM, cortisol 1 µM) and BM positive control (mDM + bosentan 100 µM, mifepristone 10 µM) and GEC+BM conditions were performed. The remaining wells were treated with mDM plus the test compound at 1 µM. 1 well was used per drug. Following 12 hours of treatment, medium was removed and cells were prepared for molecular phenotyping.
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| Growth protocol |
Human iPSC lines were derived from anonymized human skin biopsies following full informed consent and approval by the Partners Healthcare Human Research Committee (Protocol number 2010-P-000122/1). iPSC were generated by retroviral reprogramming using OCT4, SOX2, KLF4 and C-MYC and checked for pluripotency and normality of karyotype. iPSC lines were transferred to CDI (Madison, Wisconsin) for differentiation into cardiomyocytes. Following cardiomyocyte production, culture protocols were identical to those used for the standard cardiomyocytes.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cell were harvested 12 after compound addition by removing the culture medium. Cell lysates in 50 µl RLT buffer (QIAGEN, Hombrechtikon, Switzerland) were immediately frozen and stored at -80°C.
10 ng of total RNA from each sample were reverse transcribed to cDNA by poly-A-priming followed by PCR pre-amplification (15 cycles) according to the protocol supplied with the Ion AmpliSeq™ RNA Library Kit (Life Technologies, Carlsbad, USA, Catalog number 4482335). After primer digestion, adapters and molecular barcodes were ligated to the amplicons followed by magnetic bead purification. This library was amplified, purified and stored at -20°C. Amplicon size and DNA concentration were measured using an Agilent High Sensitivity DNA Kit (Agilent Technologies, Waldbronn, Germany) according to the manufacturer’s recommendation.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
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| Data processing |
Base-calling, filtering, QC, and alignment was handled automatically by IonTorrent Server Suite (version 4.0.2)
Amplicon coverage is reported by IonTorrent Server Suite (version 4.0.2) as a tab-delimited file, which was converted into GCT format by in-house scripts.
Genome_build: hg19
Supplementary_files_format_and_content: GCT format, with amplicon counts for pathway reporter genes in each sample
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| Submission date |
Nov 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jitao David Zhang |
| E-mail(s) |
jitao_david.zhang@roche.com
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| Phone |
+41616886251
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| Organization name |
F. Hoffmann-La Roche
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| Department |
Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel
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| Lab |
Pharmaceutical Sciences
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| Street address |
Grenzacherstrasse 124
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| City |
Basel |
| ZIP/Postal code |
4070 |
| Country |
Switzerland |
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| Platform ID |
GPL17301 |
| Series (1) |
| GSE89972 |
Molecular phenotyping empowers drug discovery: a proof-of-concept study |
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| Relations |
| BioSample |
SAMN06028605 |
| SRA |
SRX2355300 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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