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Sample GSM5048918 Query DataSets for GSM5048918
Status Public on Feb 24, 2021
Title 35: D10 0.3 8181
Sample type SRA
 
Source name Primary human hepatocytes
Organism Homo sapiens
Characteristics donor: 8181
dose (um): 0.3
hbv: 21P
day: 10
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.
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.
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
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
 
Submission date Jan 28, 2021
Last update date Feb 24, 2021
Contact name Ricardo Ramirez
Organization name Gilead Sciences, Inc.
Street address 333 Lakeside Drive
City Foster City
State/province CA
ZIP/Postal code 94404
Country USA
 
Platform ID GPL16791
Series (1)
GSE165727 Characterization of a KDM5 Small Molecule Inhibitor with Antiviral Activity against Hepatitis B Virus
Relations
BioSample SAMN17616153
SRA SRX9971163

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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