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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
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)
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
Relations
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
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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