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| Status |
Public on Mar 15, 2021 |
| Title |
KO_Kidney_Rep2 |
| Sample type |
SRA |
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| Source name |
HNF4AKO_Kidney
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| Organism |
Mus musculus |
| Characteristics |
tissue: Kidney
genotype: UBC-CreERT2; Hnf4af/f (HNF4AKO)
treatment: tamoxifen 100mg/kg/day
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| Treatment protocol |
Experimental UBC-CreERT2 positive and negative mice (5 weeks old) were all treated with tamoxifen at 100 mg/kg/day by intraperitoneal injection for 4 consecutive days. Kidney tissues were collected 7 days after the first injection
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted from kidney tissues of indicated genotypes. The whole kidney samples were washed with PBS, and then quick frozen in liquid nitrogen and stored at -80°C for later processing for RNA extraction. Kidney samples were homogenized in Trizol (Invitrogen) and processed for RNA extraction according to the manufacturer’s instructions.
BGI in-house kit (BGI-Shenzhen, China)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
MGISEQ-2000
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| Data processing |
Read alignment and mapping done with TopHat2, version 2.1.0
Gene and transcript level computation done with CuffQuant, Version 2.2.1
Normalized abundance measurements generated by CuffNorm, Version 2.2.1, calculate FPKM values using quartile normalization
CuffDiff, Version 2.2.1, geometric normalization, per-condition dispersion
Genome_build: mm9
Supplementary_files_format_and_content: Kidney_HNF4AKOvsCtrl_gene_exp.diff containing significant changes in transcript expression outputted by Cuffdiff
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| Submission date |
Sep 14, 2020 |
| Last update date |
Mar 15, 2021 |
| Contact name |
Michael P Verzi |
| Organization name |
Rutgers, the State University of New Jersey
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| Department |
Genetics
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| Lab |
Verzi
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| Street address |
145 Bevier Road
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| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE157911 |
Transcriptional profiles of kidney upon HNF4A loss in mice by RNA-seq |
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| Relations |
| BioSample |
SAMN16129330 |
| SRA |
SRX9120103 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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