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| Status |
Public on Mar 08, 2019 |
| Title |
GFP_1369 |
| Sample type |
SRA |
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| Source name |
GFP_liver
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
age: 11-12 weeks
transgene expressed: GFP
nutritional status: 24h fasted
tissue: Liver
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| Treatment protocol |
8-week-old C57BL/6J mice were injected with 2.5*10^11 particles of adeno-associated virus carrying mouse Nudt7 or GFP in 150 µl of sterile phosphate buffered saline via tail vein. Liver samples were collected 3-4 weeks after the injection from mice that were fasted for 24 h
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| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were removed, flash frozen in liquid nitrogen and stored at -80 C until processed. RNA was extracted using Trizol reagent.
Libraries were built using 500 ng of RNA as input material for the stranded mRNA library preparation kit from KAPA Biosystems following the manufacturer’s recommended protocol with 9 cycles of PCR
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
Read quality was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc) and deemed to require no trimming
The reads were quantified using Salmon (Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., and Kingsford, C., 2017, Nature methods 14, 417-419) with transcripts obtained from ensemble, version GRCm38.84
Using tximport (Soneson, C., Love, M. I., and Robinson, M. D., 2015, F1000Res 4, 1521) the data was imported into R and differential expression was computing using DESeq2 (Love, M. I., Huber, W., and Anders, S., 2014, Genome Biol 15, 550)
Genome_build: Ensembl, version GRCm38.84
Supplementary_files_format_and_content: sf.txt files produced by salmon give a list of Ensembl transcript IDs with TPM and estimated number of counts.
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| Submission date |
Jan 17, 2019 |
| Last update date |
Mar 08, 2019 |
| Contact name |
Roberta Leonardi |
| E-mail(s) |
[email protected]
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| Organization name |
West Virginia University
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| Street address |
1 Medical Center Drive
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| City |
Morgantown |
| State/province |
WV |
| ZIP/Postal code |
26501 |
| Country |
USA |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE125237 |
Effect of Nudt7 overexpression on the global transcriptome of mouse liver in the fasted state |
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| Relations |
| BioSample |
SAMN10762809 |
| SRA |
SRX5257671 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3566924_GFP_1369.quant.sf.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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