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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 (ChIP-Seq) |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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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 impact of CTCF insulator disruptions, we established derivatives of the GIST-T1 cell line. We then performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for CTCF, H3K27ac and H3K27me3 in GIST-T1 WT and insulator KO cell lines.
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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) |
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| Samples (45)
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| GSM7745665 |
GIST-T1, InsG, CTCF, rep1 |
| GSM7745666 |
GIST-T1, InsH, CTCF, rep1 |
| GSM7745667 |
GIST-T1, control, CTCF, rep2 |
| GSM7745668 |
GIST-T1, InsE, CTCF, rep2 |
| GSM7745669 |
GIST-T1, InsF, CTCF, rep2 |
| GSM7745670 |
GIST-T1, InsG, CTCF, rep2 |
| GSM7745671 |
GIST-T1, InsH, CTCF, rep2 |
| GSM7745672 |
GIST-T1, control, H3K27ac, rep1 |
| GSM7745673 |
GIST-T1, InsE, H3K27ac, rep1 |
| GSM7745674 |
GIST-T1, InsF, H3K27ac, rep1 |
| GSM7745675 |
GIST-T1, InsG, H3K27ac, rep1 |
| GSM7745676 |
GIST-T1, InsH, H3K27ac, rep1 |
| GSM7745677 |
GIST-T1, control, H3K27ac, rep2 |
| GSM7745678 |
GIST-T1, InsE, H3K27ac, rep2 |
| GSM7745679 |
GIST-T1, InsF, H3K27ac, rep2 |
| GSM7745680 |
GIST-T1, InsG, H3K27ac, rep2 |
| GSM7745681 |
GIST-T1, InsH, H3K27ac, rep2 |
| GSM7745682 |
GIST-T1, control, H3K27me3, rep1 |
| GSM7745683 |
GIST-T1, InsE, H3K27me3, rep1 |
| GSM7745684 |
GIST-T1, InsF, H3K27me3, rep1 |
| GSM7745685 |
GIST-T1, InsG, H3K27me3, rep1 |
| GSM7745686 |
GIST-T1, InsH, H3K27me3, rep1 |
| GSM7745687 |
GIST-T1, control, H3K27me3, rep2 |
| GSM7745688 |
GIST-T1, InsE, H3K27me3, rep2 |
| GSM7745689 |
GIST-T1, InsF, H3K27me3, rep2 |
| GSM7745690 |
GIST-T1, InsG, H3K27me3, rep2 |
| GSM7745691 |
GIST-T1, InsH, H3K27me3, rep2 |
| GSM7745692 |
GIST-T1, control, WCE, rep1 |
| GSM7745693 |
GIST-T1, InsE, WCE, rep1 |
| GSM7745694 |
GIST-T1, InsF, WCE, rep1 |
| GSM7745695 |
GIST-T1, InsG, WCE, rep1 |
| GSM7745696 |
GIST-T1, InsH, WCE, rep1 |
| GSM7745697 |
GIST-T1, control, WCE, rep2 |
| GSM7745698 |
GIST-T1, InsE, WCE, rep2 |
| GSM7745699 |
GIST-T1, InsF, WCE, rep2 |
| GSM7745700 |
GIST-T1, InsG, WCE, rep2 |
| GSM7745701 |
GIST-T1, InsH, WCE, rep2 |
| GSM7745702 |
GIST-T1, WT, CTCF, rep1 |
| GSM7745703 |
GIST-T1, WT, CTCF, rep2 |
| GSM7745704 |
GIST-T1, WT, H3K27ac, rep1 |
| GSM7745705 |
GIST-T1, WT, H3K27ac, rep2 |
| GSM7745706 |
GIST-T1, WT, WCE, rep1 |
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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 |
PRJNA1010763 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE241924_RAW.tar |
15.2 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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