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Series GSE133928 Query DataSets for GSE133928
Status Public on Aug 24, 2020
Title A topological atlas reveals layers of genome reorganization in colorectal cancer
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary To understand how nuclear architecture is altered in cancer, we profiled genome topology along with DNA methylation, chromatin modifications and the DNA binding factors CTCF in primary colon tumors, normal colon and colon cancer cell lines.
Overall design Our in vitro models included colon cancer cell lines (HCT116, SW480, RKO, LS-174T) and a line derived from normal colon (FHC).

**Due to patient privacy concerns, raw data for patient samples have been submitted to dbGAP.**
Contributor(s) Johnstone SE, Reyes A, Aryee M, Bernstein BE
Citation(s) 32841603
Submission date Jul 08, 2019
Last update date Nov 23, 2020
Contact name Alejandro Reyes
Organization name Novartis Institutes For BioMedical Research
Department Data Sciences
Street address Fabrikstrasse 22
City Basel
ZIP/Postal code 4056
Country Switzerland
Platforms (3)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (175)
GSM3930213 BRD3162-CTCF_ChIP-seq
GSM3930214 BRD3162-K27Ac_ChIP-seq
GSM3930215 BRD3162-WCE_ChIP-seq
BioProject PRJNA553150
SRA SRP214469

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
GSE133928_RAW.tar 327.0 Gb (http)(custom) TAR (of BEDPE, BW, CPG, MATRIX, TXT)
GSE133928_binAnnotation.bed.gz 464.7 Kb (ftp)(http) BED
GSE133928_binAnnotation100Kb.bed.gz 177.6 Kb (ftp)(http) BED
GSE133928_chip_input_pairing.txt.gz 298 b (ftp)(http) TXT
GSE133928_chip_input_pairing_batch2.txt.gz 163 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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