 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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 (RNA-Seq) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| 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.
|
| |
|
| Overall design |
To investigate the impact of CTCF insulator disruptions in SDH-intact cells, we established derivatives of the GIST-T1 cell line. We then performed gene expression profiling analysis between WT and insulator KO cell lines using data obtained from RNA-seq.
|
| |
|
| Contributor(s) |
Kim KL, Bernstein BE |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Aug 30, 2023 |
| Last update date |
Mar 06, 2024 |
| Contact name |
Kyung Lock Kim |
| E-mail(s) |
postclassic@gmail.com
|
| Phone |
6177589374
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Cancer Biology
|
| Lab |
Bradley E. Bernstein
|
| Street address |
450 Brookline Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platforms (1) |
|
| Samples (10)
|
| GSM7745720 |
GIST-T1, InsG, rep1 |
| GSM7745721 |
GIST-T1, InsH, rep1 |
| GSM7745722 |
GIST-T1, control, rep2 |
| GSM7745723 |
GIST-T1, InsE, rep2 |
| GSM7745724 |
GIST-T1, InsF, rep2 |
| GSM7745725 |
GIST-T1, InsG, rep2 |
| GSM7745726 |
GIST-T1, InsH, rep2 |
|
| This SubSeries is part of SuperSeries: |
| GSE241927 |
Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation |
|
| Relations |
| BioProject |
PRJNA1010764 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE241926_RAW.tar |
25.2 Mb |
(http)(custom) |
TAR (of RESULTS) |
| GSE241926_Summary_FGFins_RNA.genes.TPM.txt.gz |
2.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...