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| Status |
Public on Jan 24, 2018 |
| Title |
Genomic and epigenomic characterization of regenerating hepatocytes |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
To gain a deeper understanding of the genetic basis of liver repopulation after injury, we utilize an innovative technique to profile the expression changes and chromatin landscape during the regenerative response. We utilize the Fah-/- mouse, a model for hereditary tyrosinemia deficient in fumarylacetoacetate hydrolase (FAH), that undergoes repopulation with FAH-expressing hepatocytes. We employ translating ribosome affinity purification followed by RNA-sequencing (TRAP-seq) and assay for transposase accessible chromatin using sequencing (ATAC-seq) to specifically isolate regenerating hepatocytes and performed high-throughput sequencing to identify the dynamic genomic and epigenomic changes during liver repopulation.
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| Overall design |
A total of 16 mice was used for the TRAP-seq study (n=4, quiescent; n=3, 1-week injury; n=6, 4-week injury; n=3, 4-week severe injury). A total of 7 mice was used for the ATAC-seq study (n=2, quiescent; n=4, 1-week injury)
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| Contributor(s) |
Wang AW, Wangensteen KJ, Wang JY, Kaestner KH |
| Citation(s) |
29517978, 31629814 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| F31 DK113666 |
Elucidating Redox Regulation in the Repopulating Liver |
UNIVERSITY OF PENNSYLVANIA |
Amber Weiching Wang |
| R01 DK102667 |
Innovative Genetic Approaches for Hepatic Repopulation |
UNIVERSITY OF PENNSYLVANIA |
KLAUS H. KAESTNER |
| K08 DK106478 |
Genetic basis of liver repopulation |
UNIVERSITY OF PENNSYLVANIA |
Kirk J Wangensteen |
| T32 GM008076 |
Predoctoral Training Grant in Pharmacology |
UNIVERSITY OF PENNSYLVANIA |
Julie Ann Blendy |
| P30 DK050306 |
Center for Molecular Studies in Digestive and Liver Diseases |
UNIVERSITY OF PENNSYLVANIA |
Anil K Rustgi |
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| |
| Submission date |
Jan 23, 2018 |
| Last update date |
Nov 20, 2019 |
| Contact name |
Amber Wang |
| E-mail(s) |
wamber@upenn.edu
|
| Phone |
2674323958
|
| Organization name |
University of Pennsylvania
|
| Department |
Genetics
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| Lab |
Klaus Kaestner
|
| Street address |
3400 Civic Center Blvd, SCTR 12-164
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (26)
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| Relations |
| BioProject |
PRJNA431154 |
| SRA |
SRP131108 |
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