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Series GSE241926 Query DataSets for GSE241926
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
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Submission date Aug 30, 2023
Last update date Mar 06, 2024
Contact name Kyung Lock Kim
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)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (10)
GSM7745717 GIST-T1, control, rep1
GSM7745718 GIST-T1, InsE, rep1
GSM7745719 GIST-T1, InsF, rep1
This SubSeries is part of SuperSeries:
GSE241927 Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation
BioProject PRJNA1010764

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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
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Raw data are available in SRA
Processed data provided as supplementary file

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