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| Status |
Public on Mar 06, 2024 |
| Title |
Dissection of a CTCF insulator and its impact on chromosome topology and oncogene expression in gastrointestinal stromal tumor (micro-C) |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
Enhancer-Promoter communication is dependent on the topological organization of genomic DNA, including topologically-associated domains (TADs) and boundaries enforced by the CTCF insulator protein. Here, we characterized the structure and function of the FGF3/4 locus and the boundary element that insulates the region from an enhancer in the adjacent TAD.
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| Overall design |
To investigate the topological impact of CTCF insulator disruptions, we established derivatives of the GIST-T1 cell line. We then performed region-capture micro-C assay in GIST-T1 WT and insulator KO cells.
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| Contributor(s) |
Kim KL, Bernstein BE |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Aug 30, 2023 |
| Last update date |
Mar 06, 2024 |
| Contact name |
Kyung Lock Kim |
| E-mail(s) |
postclassic@gmail.com
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| Phone |
6177589374
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| Organization name |
Dana-Farber Cancer Institute
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| Department |
Cancer Biology
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| Lab |
Bradley E. Bernstein
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| Street address |
450 Brookline Avenue
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (10)
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| GSM7745710 |
GIST-T1, InsG, RCMC rep1 |
| GSM7745711 |
GIST-T1, InsH, RCMC rep1 |
| GSM7745712 |
GIST-T1, control, RCMC rep2 |
| GSM7745713 |
GIST-T1, InsE, RCMC rep2 |
| GSM7745714 |
GIST-T1, InsF, RCMC rep2 |
| GSM7745715 |
GIST-T1, InsG, RCMC rep2 |
| GSM7745716 |
GIST-T1, InsH, RCMC rep2 |
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| This SubSeries is part of SuperSeries: |
| GSE241927 |
Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation |
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| Relations |
| BioProject |
PRJNA1010765 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE241925_RAW.tar |
388.7 Mb |
(http)(custom) |
TAR (of HIC) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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