|
Status |
Public on Jan 06, 2021 |
Title |
S9 fast |
Sample type |
SRA |
|
|
Source name |
Liver
|
Organisms |
Homo sapiens; Mus musculus |
Characteristics |
condition: fast 24h from 9:00am to 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 |
SAMN11539830 |
SRA |
SRX5771759 |