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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 28, 2023 |
| Title |
LncRNA EPR transcriptional activity controls intestinal mucus and prevents susceptibility to inflammation and tumorigenesis [Hi-C] |
| Organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
We have previously shown that EPR favors the interaction between Mettl7a1 promoter and a distal enhancer element. To comprehensively map long-range interactions between promoters and distal regulatory elements that are affected by EPR KO in large intestine, we preformed Promoter capture Hi-C experiments. Crypts were purified from proximal colon of two EPR fl/fl control and two EPR cKO mice. Hi-C libraries were constructed and hybridized with biotinylated RNA probes from the Arima mouse promoter panel designed to hybridize the promoters of 25752 mouse genes. Captured libraries were sequenced and bioinformatically analyzed. Our results indicate that EPR knockout leads to a rewiring of a number of promoter-enhancer interactions.
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| Overall design |
Crypts from proximal colon were isolated from three distinct EPR fl/fl and three EPR cKO mice, snap-frozen and shipped to Arima Genomics (San Diego, CA) where the experiments were conducted. Briefly, chromatin from crypts was crosslinked and digested using a restriction enzyme cocktail. The 5’-overhangs are then filled in, causing the digested ends to be labeled with a biotinylated nucleotide. Next, spatially proximal digested ends of DNA are ligated, capturing the sequence and structure of the genome. The ligated DNA is then purified, producing pure proximally-ligated DNA. The proximally-ligated DNA is then fragmented, and the biotinylated fragments are enriched. The enriched fragments are then subjected to a custom library preparation protocol utilizing the Arima Library Prep Module . Following Library prep we perform shallow sequencing (500k-2M paired-end reads) to assess the libraries’ quality in terms of library complexity and long-range interaction information prior to proceeding with the capture. Once Hi-C is complete, the sample is pre-cleared to remove carry over biotinylated Hi-C molecules. The interactions of interest are then enriched using biotinylated RNA probes from the Arima Mouse Promoter Panel .
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| Contributor(s) |
Briata P, Zapparoli E, Bucci G, Inga A, Chiacchiera F, Caputo L, Gherzi R |
| Citation(s) |
37070602 |
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| Submission date |
Dec 07, 2022 |
| Last update date |
Jun 27, 2023 |
| Contact name |
gabriele bucci |
| E-mail(s) |
bucci.gabriele@hsr.it
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| Phone |
+39026439140
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| Organization name |
IRCCS Ospedale San Raffaele
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| Department |
CTGB
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| Street address |
via olgettina 58
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| City |
Milano |
| State/province |
MI |
| ZIP/Postal code |
20100 |
| Country |
Italy |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE220310 |
LncRNA EPR transcriptional activity controls intestinal mucus and prevents susceptibility to inflammation and tumorigenesis |
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| Relations |
| BioProject |
PRJNA909615 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE220309_RAW.tar |
349.0 Mb |
(http)(custom) |
TAR (of BIGWIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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