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Sample GSM6337564 Query DataSets for GSM6337564
Status Public on Jul 15, 2022
Title 10_HBV_RO22_100nM_3h
Sample type SRA
 
Source name HBV-infected hepatocytes Veh RO22 3h
Organism Hepatitis B virus
Characteristics cell type_used_for_viral_infection: Hepatocyte
cell genotype: WT
treatment: RO22
time: 3h
Extracted molecule total RNA
Extraction protocol Cell were harvested 3h, 6h, 12h, and 24h 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.
For ribosomal RNA depletion the RiboZero magnetic Gold kit (Illumina) was used. Quality of amplified libraries was accessed by capillary electrophoresis with a high sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies) and quantified by quantitative PCR with a sequencing library quantification kit (KAPA Biosystems) on a Roche Light Cycler 480. Multiplexed libraries with 1 % spiked in PhiX control were sequenced on a HiSeq2500 instrument for 50 cycles using version 4 chemistry reagents (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Linker tags were removed from RNA sequencing by the FASTX Toolkit, v0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/).
Reads mapped to the human genome are removed. The STAR aligner (version 2.6.1d) and the human reference genome GRch38.p12 is used.
The remaining reads were analyzed with HBVouroboros.
Assembly: HBV genomes in HBVdb are used as part of the HBVouroboros
Supplementary files format and content: infref_genome_depth.tsvthe contains values that arethe number of reads at each genomic position of the automatically inferred HBV genotype.
 
Submission date Jul 13, 2022
Last update date Aug 31, 2022
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 GPL32478
Series (1)
GSE208115 Effect of two compounds on HBV gene expression in HBV-infected primary human hepatocytes.
Relations
BioSample SAMN29714978
SRA SRX16175803

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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