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Series GSE128676 Query DataSets for GSE128676
Status Public on Dec 01, 2020
Title Genome-wide chromatin interactions identify characteristic promoter-distal loops
Organism Homo sapiens
Experiment type Other
Summary We developed a novel computational model, HiSIF (Hi-C Significant Interacting Fragments), which uses a Poisson Mixture Model (PMM) with a power-law decay background. We compared its performance to some existing programs with publicly available Hi-C data, and then applied it to in situ Hi-C data in breast cancer sensitive and resistant cells.
Overall design In this study, we tested the model in our newly generated Hi-C data in three ERĪ± positive breast cancer cell lines, MCF7, tamoxifen-resistant MCF7 (MCF7-TamR) (MCF7 and MCF7-TamR data have been deposited in GEO under accession number GSE108787), T47D and tamoxifen-resistant T47D (T47D-TamR), ZR75-1 and tamoxifen-resistant ZR75-1 (ZR75-1-TamR).
Contributor(s) Zhou Y, Jin V
Citation(s) 32956836
Submission date Mar 21, 2019
Last update date Dec 01, 2020
Contact name Yufan Zhou
Organization name UT health Science Center at San Antonio
Street address 7703 Floyd Curl Dr
City San Antonio
State/province TX
ZIP/Postal code 78229
Country USA
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (4)
GSM3682155 T47D parental
GSM3682156 T47D Tamoxifen Resistant
GSM3682157 ZR75-1 parental
BioProject PRJNA528483
SRA SRP189090

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE128676_RAW.tar 17.6 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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