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Status |
Public on Dec 01, 2022 |
Title |
liver, patient11, week24 |
Sample type |
SRA |
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Source name |
liver
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Organism |
Homo sapiens |
Characteristics |
tissue: liver cell line: patient11 treatment: Tenofovir Alafenamide timepoint: week24
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
Oct 21, 2022 |
Last update date |
Dec 01, 2022 |
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 |
GPL24676 |
Series (1) |
GSE216314 |
Longitudinal liver sampling in patients with chronic hepatitis B starting antiviral therapy reveals hepatotoxic CD8+ T cells |
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Supplementary data files not provided |
Raw data not provided for this record |
Processed data are available on Series record |
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