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Sample GSM1574752 Query DataSets for GSM1574752
Status Public on Jul 01, 2015
Title PHH1_Compound_1uM IonXpress_009
Sample type SRA
 
Source name primary human hepatocytes
Organism Homo sapiens
Characteristics individual: PHH1
cell type: primary human hepatocytes
treatment: Compound 1uM
rna conc: 52.7
library concentration: 12854.3
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).
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Description IonXpress_009
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
 
Submission date Dec 30, 2014
Last update date May 15, 2019
Contact name Jitao David Zhang
E-mail(s) jitao_david.zhang@roche.com
Phone +41616886251
Organization name F. Hoffmann-La Roche
Department Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel
Lab Pharmaceutical Sciences
Street address Grenzacherstrasse 124
City Basel
ZIP/Postal code 4070
Country Switzerland
 
Platform ID GPL17303
Series (1)
GSE64588 Molecular phenotyping of a test compound (small-molecule neurotransmitter receptor antagonist) in primary human hepatocytes
Relations
BioSample SAMN03274055
SRA SRX825696

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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