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| Status |
Public on Jul 01, 2015 |
| Title |
PHH2_Compound_3uM IonXpress_039 |
| Sample type |
SRA |
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| Source name |
primary human hepatocytes
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| Organism |
Homo sapiens |
| Characteristics |
individual: PHH2
cell type: primary human hepatocytes
treatment: Compound 3uM
rna conc: 17.647
library concentration: 13683.5
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| Treatment protocol |
Cells were exposed to test compounds or vehicle (0.1% DMSO) after over-night pre-culture in William’s Medium E (Sigma-Aldrich, Buchs, Switzerland) supplemented with Penicillin/Streptomycin (Life Technologies, Zug, Switzerland).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cell were harvested 3h after test 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 time point and biological replicate was reverse transcribed to cDNA and amplified by limited PCR according to the protocol supplied with the Ion AmpliSeq™ RNA Library Kit (Life Technologies, Carlsbad, USA, Catalog number 4482335). After primer digestion, adapters and barcodes were ligated to the amplicons followed by magnetic bead purification. The purified library was amplified, purified and stored at -20°C. Amplicon size and DNA concentration was measured using an Agilent High Sensitivity DNA Kit (Agilent Technologies, Waldbronn, Germany) according to the manufacturer's guide.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Description |
IonXpress_039
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| Data processing |
Base-calling, filtering, and alignment is 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
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| Submission date |
Dec 30, 2014 |
| 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 |
GPL17303 |
| Series (1) |
| GSE64588 |
Molecular phenotyping of a test compound (small-molecule neurotransmitter receptor antagonist) in primary human hepatocytes |
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| Relations |
| BioSample |
SAMN03274081 |
| SRA |
SRX825722 |
| 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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