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Sample GSM6737752 Query DataSets for GSM6737752
Status Public on Feb 28, 2024
Title UBV PHH at 30hr rep1
Sample type SRA
 
Source name Primary human hepatocytes, mouse embryonic fibroblasts
Organisms Homo sapiens; Mus musculus
Characteristics tissue: Primary human hepatocytes, mouse embryonic fibroblasts
cell line: Primary Human Hepatocytes [BioIVT donor: UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]
cell type: primary human hepatocyte, mouse embryonic fibroblast
genotype: WT
treatment: circadian synchronization and RNA extraction
time: 30 hours post-synchronization
Treatment protocol To perform circadian synchronization, the cultures were placed in Non-HEPES-buffered CO2 Independent Medium (COI, Thermofisher) with 10% (v/v) fetal bovine serum (FBS, Gemini), 1% (v/v) ITS+ (insulin/ human transferrin/selenous acid and linoleic acid) premix (BD Biosciences) and 7 ng/ml glucagon (Sigma)
Growth protocol Hepatocytes were maintained in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM with L-glutamine, Corning) with 10% (v/v) fetal bovine serum (FBS, Gemini), 1% (v/v) ITS+ (insulin/ human transferrin/selenous acid and linoleic acid) premix (BD Biosciences), 7 ng/ml glucagon (Sigma), 40 ng/ml dexamethasone (Sigma), 15 mM HEPES (Gibco), and 1% (v/v) penicillin-streptomycin (Corning). J2-3T3 male murine embryonic fibroblasts were cultured at <18 passages in fibroblast medium comprising of DMEM with high glucose, 10% (v/v) bovine serum (Thermo Fisher), and 1% (v/v) penicillin-streptomycin (Corning). Primary human hepatocytes were seeded on collagen-coated micropatterned plates as detailed previously (March et al., 2015).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIzol (Thermo Fisher) and purified using RNeasy Mini Kit (Qiagen)
RNA integrity was determined using an Agilent Fragment Analyzer and purity and quantity determined using a Thermo Scientific Nanodrop1000 Spectrophotometer. High throughput RNAseq libraries were prepared as previously described (M using 100ng of total RNA input and sequenced on a NovaSeq6000 using 50nt paired-end sequencing
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Illumina NovaSeq 6000 using v3 chemistry. NovaSeq Software: Control v1.6.0, RTA 3.4.4. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Gene expression was quantified using RSEM version 1.3.1 and STAR version 2.7.1a alignment to a transcriptome derived from the human hg38 primary assembly and ensembl version 98 annotation.
Assembly: hg38 with the ensembl 98 annotation
Supplementary files format and content: 190712Bha_set1_intCt.txt.gz is a tab delimited text file of integer count data
Supplementary files format and content: 190712Bha_set1_l2tpm.txt.gz is a tab delimited text file of log2 tpm data including a +1 offset
 
Submission date Nov 17, 2022
Last update date Feb 28, 2024
Contact name Charles Arthur Whittaker
E-mail(s) charliew@mit.edu
Organization name Koch Institute
Street address 77 Mass Ave 76-189
City Cambridge
State/province MA
ZIP/Postal code 02152
Country USA
 
Platform ID GPL25526
Series (2)
GSE218242 Circadian rhythm-dependent programs control inflammatory responses and drug metabolism in primary human hepatocytes I.
GSE218244 Circadian rhythm-dependent programs control inflammatory responses and drug metabolism in primary human hepatocytes
Relations
BioSample SAMN31775764
SRA SRX18298322

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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