|
| Status |
Public on Jul 15, 2022 |
| Title |
08_HBV_Veh_0nM_3h |
| Sample type |
SRA |
| |
|
| Source name |
HBV-infected hepatocytes Veh 3h
|
| Organism |
Hepatitis B virus |
| Characteristics |
cell type_used_for_viral_infection: Hepatocyte
cell genotype: WT
treatment: Veh
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 |
SAMN29714980 |
| SRA |
SRX16175801 |
