NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3741764 Query DataSets for GSM3741764
Status Public on Jan 06, 2021
Title S1 fed
Sample type SRA
 
Source name Liver
Organisms Homo sapiens; Mus musculus
Characteristics condition: ad libitum harvest at 9:00am
tissue: Human Liver cells xenografted into TKNOG mice
Treatment protocol TK-NOG mice, in which a herpes simplex virus type 1 thymidine kinase (TK) transgene under a mouse albumin promoter is expressed within the liver of highly immune-deficient NOG mice, were obtained from Taconic Biosciences. The TK converts an antiviral medication ganciclovir (GCV) into a toxic product that allows selective elimination of TK positive cells in vivo. The cryopreserved primary human hepatocytes were obtained from Thermo Fisher Scientific. The humanized TK-NOG mice were prepared as previously described (Hasegawa, M. et al.). Briefly, The TK-NOG mice at 8-9 weeks old received an i.p. injection of GCV at a dose of 25 mg/kg. One week later, 50ul volume of 1 106 human primary hepatocytes suspended in HBSS solution were transplanted via intra-splenic injection. 8-12 weeks after transplantation, the serum human albumin in the mice were measured as an index of the extent of human hepatocytes replacement. Humanized TK-NOG mice with serum human albumin levels above 0.5 mg/ml were used for experiments, in which human hepatic genes could be reliably detected by q-PCR. Reference paper PMID: 21238430.
Extracted molecule total RNA
Extraction protocol Whole livers were removed from the humanized mice either with ad libitum, a 24h fasting, or a 24h fasting followed by a 4h refeeding. The livers were flash frozen and powdered in liquid nitrogen, and the RNA was harvested using Trizol reagent.  Strand specific sequencing libraries were constructed using illumine TruSeq RNA sample Prep kit.
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing trimgalore with options '-p --illumina' to trim reads
HISAT2 align with options '-p --no-mixed --no-discordant' to align to GRCh38 + GRCm38 combined reference genome
Sambamba view to reformat aligned reads from .sam to .bam and sambamba sort to sort reads by coordinate
subread featureCounts with options '-p -P -s2' using Gencode H29 reference annotation to generate raw gene counts for aligned files
Genome_build: GRCh38 + GRCm38
Supplementary_files_format_and_content: tab delimited text file includes raw gene counts for each sample
 
Submission date Apr 30, 2019
Last update date Jan 06, 2021
Contact name Haiming Cao
E-mail(s) haiming.cao@nih.gov
Phone 3014029032
Organization name NIH
Department NHLBI
Lab Laboratory of Obesity and Metabolic Diseases
Street address 9000 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL24496
Series (2)
GSE130525 Fasting/fed/refeeding RNAseq experiment conducted on mice with xenografted human livers.
GSE224281 Single molecule-level metabolic responsive landscape of human liver transcriptome
Relations
BioSample SAMN11539838
SRA SRX5771751

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap