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Sample GSM6529658 Query DataSets for GSM6529658
Status Public on Sep 17, 2022
Title NTC-20200923
Sample type SRA
 
Source name No tmeplate control
Organism blank sample
Characteristics sample type: No tmeplate control
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
 
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: vcf files: variant calling
 
Submission date Aug 31, 2022
Last update date Sep 18, 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 GPL30314
Series (1)
GSE212418 RNA sequences amplified from a HBV-genome-encoding plasmid
Relations
BioSample SAMN30616177
SRA SRX17382648

Supplementary file Size Download File type/resource
GSM6529658_infref_NTC-20200923_cleaned_allelicprimitives.vcf.gz 2.0 Kb (ftp)(http) VCF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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