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Sample GSM7441029 Query DataSets for GSM7441029
Status Public on Jun 07, 2023
Title liver, patient10, week0
Sample type SRA
 
Source name liver
Organism Hepatitis B virus
Characteristics disease state: Hepatitis B
tissue: liver
time: week0
treatment: Tenofovir Alafenamide
Extracted molecule polyA RNA
Extraction protocol After taking FNAs from the patients, samples were maintained on ice and immediately processed. After quality control steps, red blood cells were removed by 5 min incubation with Red Blood Cell Lysis Buffer (BioLegend) and subsequent 10x dilution with PBS. Cells were washed, counted, and subjected to scRNAseq.
Samples were prepared as outlined by the 10x Genomics Single Cell 5’ Reagent Kit user guide.
The molarity of each library was calculated based on library size as measured by the Bioanalyzer (Agilent Technologies) and qPCR amplification data. Samples were pooled and adjusted to 10 nM, then diluted to 2 nM. Each 2 nM pool was denatured. Library pools were further diluted to a final loading concentration of 14 pM. 150 μl were loaded into each well of an 8-well strip tube and loaded onto a cBot (Illumina) for cluster generation. Samples were sequenced on the HiSeq 2500 (Illumina) system.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Viral reads were identified using Viral-Track from the 10X Genomics scRNA-Seq of fine needle aspirates from the liver of patients treated with Tenofovir Alafenamide
Data processing The viral read filtering and alignment were performed using Viral-Track(https://github.com/PierreBSC/Viral-Track)using the viruSITE database (http://www.virusite.org/index.php)
Assembly: viruSITE database (release2020.3)
Supplementary files format and content: Alignment files for Hepatitis B viral reads in BAM format
Supplementary files format and content: Viral read coverage matrix files in text format
 
Submission date Jun 02, 2023
Last update date Jun 07, 2023
Contact name Adam Gehring
E-mail(s) adam.gehring@uhnresearch.ca
Organization name UHN
Street address 101 College St
City Toronto
State/province ON
ZIP/Postal code M5G 1L7
Country Canada
 
Platform ID GPL32478
Series (1)
GSE234015 Efficacy of antiviral therapy and host-virus interactions visualized using serial liver sampling with fine-needle aspirates

Supplementary file Size Download File type/resource
GSM7441029_010_WEEK0_hbv_coverage.tsv.gz 7.8 Kb (ftp)(http) TSV
GSM7441029_010_wk0_hbv.bam 355.6 Kb (ftp)(http) BAM
Raw data not provided for this record
Processed data provided as supplementary file

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