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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 17, 2022 |
| Title |
HBV-POS1-LOD4-20200922 |
| Sample type |
SRA |
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| Source name |
A plasmid containing cloned HBV genome
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| Organism |
Hepatitis B virus |
| Characteristics |
sample type: A plasmid containing cloned HBV genome
genotype: U95551 (WT), with modifications: C673T and A838C
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| Extracted molecule |
total RNA |
| Extraction protocol |
A pair of primers (forward primer sequence: ccggaaagcttgagctcttcTTTTTCACCTCTGCCTAATCA; reverse primer sequence: ccggaaagcttgagctcttcAAAAAGTTGCATGGTGCTGG) were designed based on the open loop region for long fragment amplification to cover the whole length of HBV DNA with PCR buffer of 2 × Vazyme LAmp® Master Mix (Vazyme Biotech Co. Ltd, Nanjing, China). After purification of the PCR product, long fragment HBV DNA were performed the random fragmentation via ultrasound fragmentation instrument of LE220 (Covaris, Woburn, Massachusetts) and utilized the NEXTflex Rapid DNA-Seq Kit for Illumina (Bioo Scientific, Austin, Texas) to obtain the DNA libraries. Quality of long fragment amplification products were assessed by gel electrophoresis while quality of amplified libraries was assessed by capillary electrophoresis with a DNA chip on a 2100 Bioanalyzer
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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: vcf files: variant calling
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| Submission date |
Aug 31, 2022 |
| Last update date |
Sep 18, 2022 |
| 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 |
GPL32478 |
| Series (1) |
| GSE212418 |
RNA sequences amplified from a HBV-genome-encoding plasmid |
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| Relations |
| BioSample |
SAMN30616208 |
| SRA |
SRX17382633 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6529627_infref_HBV-POS1-LOD4-20200922_cleaned_allelicprimitives.vcf.gz |
974 b |
(ftp)(http) |
VCF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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