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| Status |
Public on Jun 07, 2023 |
| Title |
liver, patient10, week12 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Hepatitis B virus |
| Characteristics |
disease state: Hepatitis B
tissue: liver
time: week12
treatment: Tenofovir Alafenamide
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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
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| 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
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| Submission date |
Jun 02, 2023 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Adam Gehring |
| E-mail(s) |
adam.gehring@uhnresearch.ca
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| Organization name |
UHN
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| Street address |
101 College St
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| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 1L7 |
| Country |
Canada |
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| Platform ID |
GPL32478 |
| Series (1) |
| GSE234015 |
Efficacy of antiviral therapy and host-virus interactions visualized using serial liver sampling with fine-needle aspirates |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM7441030_010_WEEK12_hbv_coverage.tsv.gz |
4.6 Kb |
(ftp)(http) |
TSV |
| GSM7441030_010_wk12_hbv.bam |
319.1 Kb |
(ftp)(http) |
BAM |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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