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| Status |
Public on Nov 28, 2023 |
| Title |
Profiling Sox4 binding sites and histone post-translational modifications in adult hepatocytes (CUT&RUN I) |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Recent studies have demonstrated that hepatocytes can be reprogrammed into biliary epithelial cell-like cells. An earlier work in our laboratory nominated Sox4 as an initiation factor of this reprogramming event. To investigate the effect of Sox4 on the change of chromatin landscape of hepatocytes, we exogenosly expressed Sox4 in adult hepatocytes, and profiled its binding sites in a genome wide manner by CUT&RUN-seq. We also profiled histone post-translational modifications of H3K4me1, H3K4me3, H3K27ac and H3K27me3 to explore the influence of Sox4 on the epigenetic landscape of hepatocytes.
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| Overall design |
Mice were injected with adeno-associated viruses (AAVs) packaged with mouse Sox4 (AAV8-TBG-HA-Sox4-P2A-Cre), and hepatocytes were harvested 18 hours post injection (18 hpi) and 4 days post injection (4 dpi) by a standard 2-step liberase digestion method followed by a Percoll enrichment step.
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| Contributor(s) |
Katsuda T, Sussman J, Stanger BZ |
| Citation(s) |
38409161 |
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| Submission date |
Dec 17, 2022 |
| Last update date |
Mar 11, 2024 |
| Contact name |
Takeshi Katsuda |
| E-mail(s) |
tkatsuda412@gmail.com
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| Phone |
+1-215-746-5559
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| Organization name |
University of Pennsylvania
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| Department |
Perelman School of Medicine
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| Lab |
Gastroenterology Division
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| Street address |
421 Curie Blvd, BRB II/III Rm531
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (24)
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| GSM6856394 |
Sox4_4dpi, rep1 NextSeq 500 |
| GSM6856395 |
Sox4_4dpi, rep2 NextSeq 500 |
| GSM6856396 |
Sox4_4dpi, rep3 NextSeq 500 |
| GSM6856397 |
Isotype_18hpi, rep1 NextSeq 500 |
| GSM6856398 |
Isotype_18hpi, rep2 NextSeq 500 |
| GSM6856399 |
Isotype_18hpi, rep3 NextSeq 500 |
| GSM6856400 |
Isotype_4dpi, rep1 NextSeq 500 |
| GSM6856401 |
Isotype_4dpi, rep2 NextSeq 500 |
| GSM6856402 |
Isotype_4dpi, rep3 NextSeq 500 |
| GSM6856403 |
H3K27ac_18hpi, rep1 NextSeq 500 |
| GSM6856404 |
H3K27ac_18hpi, rep2 NextSeq 500 |
| GSM6856405 |
H3K27ac_4dpi, rep1 NextSeq 500 |
| GSM6856406 |
H3K27ac_4dpi, rep2 NextSeq 500 |
| GSM6856407 |
H3K4m27me3_18hpi, rep1 NextSeq 500 |
| GSM6856408 |
H3K4m27me3_18hpi, rep2 NextSeq 500 |
| GSM6856409 |
H3K4m27me3_4dpi, rep1 NextSeq 500 |
| GSM6856410 |
H3K4m27me3_4dpi, rep2 NextSeq 500 |
| GSM6856411 |
H3K4me1_18hpi, rep1 NextSeq 500 |
| GSM6856412 |
H3K4me1_4dpi, rep1 NextSeq 500 |
| GSM6856413 |
H3K4me3_18hpi, rep1 NextSeq 500 |
| GSM6856414 |
H3K4me3_4dpi, rep1 NextSeq 500 |
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| This SubSeries is part of SuperSeries: |
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| Relations |
| BioProject |
PRJNA913431 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE221223_RAW.tar |
1.1 Gb |
(http)(custom) |
TAR (of BED, BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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