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Sample GSM6668693 Query DataSets for GSM6668693
Status Public on Dec 01, 2022
Title liver, patient10, week0
Sample type SRA
 
Source name liver
Organism Homo sapiens
Characteristics tissue: liver
cell line: patient10
treatment: Tenofovir Alafenamide
timepoint: week0
Extracted molecule total 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 single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Unique molecular identifiers (UMIs) were generated using the CellRanger Pipeline version 3.1.0 (10x Genomics). Sequencing data were aligned to GRCh38-HBV reference genome.
CellRanger-processed filtered feature matrices were analyzed using Seurat version 3.2.3.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
 
Submission date Oct 21, 2022
Last update date Dec 01, 2022
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 GPL24676
Series (1)
GSE216314 Longitudinal liver sampling in patients with chronic hepatitis B starting antiviral therapy reveals hepatotoxic CD8+ T cells

Supplementary data files not provided
Raw data not provided for this record
Processed data are available on Series record

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