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Status |
Public on Feb 24, 2021 |
Title |
35: D10 0.3 8181 |
Sample type |
SRA |
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Source name |
Primary human hepatocytes
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Organism |
Homo sapiens |
Characteristics |
donor: 8181 dose (um): 0.3 hbv: 21P day: 10
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Treatment protocol |
HBV-infected primary human hepatocytes were treated with the KDM5 inhibitor prodrug GS-5801 at 0, 0.03, 0.3, and 10 µM final concentration every three to four days for 13 days. GS-5801 was formulated in 100 % DMSO at a concentration of 10 mM.
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Growth protocol |
Cryopreserved primary human hepatocytes (PHH) isolated from multiple donors were purchased from Thermo Fisher Scientific (HMCPTS; Donors Hu8181, Hu8130, Hu4239), After thawing, cells were recovered by centrifugation at 100g through cryopreserved hepatocyte recovery medium (Thermo Fisher Scientific; CM7500) and plated in collagen coated 96-well plates (Thermo Fisher Scientific; CM1096) at a density of 65,000 – 70,000 live cells per well. Cells were plated in William’s E medium (Thermo Fisher Scientific; A1217601) supplemented with 3.6 % hepatocyte thawing and plating supplement (Thermo Fisher Scientific, A15563), 5 % fetal bovine serum (Thermo Fisher Scientific; 16000-036), 1 µM dexamethasone (Thermo Fisher Scientific, A15563), and 0.2 % Torpedo antibiotic mix (Bioreclamation; Z990008). Approximately 12 – 14 hours after plating, plating medium was removed, and cells were switched into maintenance medium: William’s E medium supplemented with 4 % hepatocyte maintenance supplement (Thermo Fisher Scientific; AI15564), 2 % fetal bovine serum, 0.1 µM dexamethasone, 1.5 % DMSO (Sigma-Aldrich, St. Louis, MO; D8418), and 0.2 % Torpedo antibiotic mix. Approximately 24 hours after plating, PHH were infected with 6 µl of patient sera containing the HBV virus (041FY67821P; genotype A) in maintenance medium supplemented with 4 % PEG 8000. Infections were allowed to proceed for 20 – 24 hours before removing remaining extracellular virions by washing with maintenance medium three times.
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Extracted molecule |
total RNA |
Extraction protocol |
RNA samples were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103). Libraries were prepared for sequencing using the Ampliseq human transcriptome kit (Thermo) for sequencing on Ion Torrent
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Data processing |
Basecalls from Illumina samples were performed using CASAVA Reads were aligned to human genome assembly hg19 using STAR 2.4 Reads per gene were quantified by RSEM Genome_build: hg19 Supplementary_files_format_and_content: Read Counts matrix with samples as columns
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Submission date |
Jan 28, 2021 |
Last update date |
Feb 24, 2021 |
Contact name |
Ricardo Ramirez |
Organization name |
Gilead Sciences, Inc.
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Street address |
333 Lakeside Drive
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City |
Foster City |
State/province |
CA |
ZIP/Postal code |
94404 |
Country |
USA |
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Platform ID |
GPL16791 |
Series (1) |
GSE165727 |
Characterization of a KDM5 Small Molecule Inhibitor with Antiviral Activity against Hepatitis B Virus |
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Relations |
BioSample |
SAMN17616153 |
SRA |
SRX9971163 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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