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Series GSE176066 Query DataSets for GSE176066
Status Public on Jan 18, 2022
Title NicE-C efficiently reveals open chromatin associated chromosome interactions at high resolution
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Enhancer-promoter communication is known to regulate spatiotemporal gene expression. Here, we present NicE-C, a method that leverages nicking enzyme mediated open chromatin profiling and chromosome conformation capture to enable robust and cost-effective detection of chromatin interactions among open chromatin regions (e.g., between enhancers and promoters). Demonstrating its application utility, NicE-C revealed dynamic enhancer-promoter interactions associated with gene expression changes after TNFÉ‘ stimulation in HeLa cells and during aging process in mice kidney.
Overall design NicE-C are generated for HeLa cells, HeLaS3 cells with or without TNFa stimulation, IMR90 cells, Mice kidney of young and old mice. RNA-seq are generated for HeLa cells, HeLaS3 cells with or without TNFa stimulation and kidney of young and old mice. HiC and NicE-seq are generated for HeLa cells.
Web link
Contributor(s) Luo Z, Zhang R, Hu T, Song X
Citation(s) 35105668
Submission date Jun 03, 2021
Last update date Apr 17, 2022
Contact name Zhengyu Luo
Phone 18709865282
Organization name USTC
Lab Song Xiaoyuan Lab
Street address Huangshan street
City HeFei
State/province AnHui
ZIP/Postal code 230026
Country China
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (32)
GSM5354334 HeLa_Hi-C_rep1
GSM5354335 HeLa_Hi-C_rep2
GSM5354336 HeLa_NicE-C_rep1
BioProject PRJNA734778
SRA SRP322418

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 988.3 Mb (ftp)(http) BW
GSE176066_HeLaS3_NicE-C_100K.hic 4.1 Gb (ftp)(http) HIC 1.8 Gb (ftp)(http) BW
GSE176066_HeLaS3_NicE-C_1M.hic 8.2 Gb (ftp)(http) HIC 635.6 Mb (ftp)(http) BW
GSE176066_HeLaS3_TNFa_NicE-C.hic 1.8 Gb (ftp)(http) HIC 191.9 Mb (ftp)(http) BW 639.0 Mb (ftp)(http) BW
GSE176066_HeLaS3_control_NicE-C.hic 1.9 Gb (ftp)(http) HIC 190.0 Mb (ftp)(http) BW
GSE176066_HeLa_Hi-C.hic 11.6 Gb (ftp)(http) HIC 3.4 Gb (ftp)(http) BW
GSE176066_HeLa_NicE-C.hic 11.9 Gb (ftp)(http) HIC 674.3 Mb (ftp)(http) BW 259.0 Mb (ftp)(http) BW 1.4 Gb (ftp)(http) BW
GSE176066_IMR90_NicE-C.hic 4.3 Gb (ftp)(http) HIC 2.1 Gb (ftp)(http) BW
GSE176066_Mice_kidney_18m_NicE-C.hic 15.4 Gb (ftp)(http) HIC 164.6 Mb (ftp)(http) BW 2.0 Gb (ftp)(http) BW
GSE176066_Mice_kidney_2m_NicE-C.hic 13.5 Gb (ftp)(http) HIC 185.2 Mb (ftp)(http) BW 816.7 Mb (ftp)(http) BW
GSE176066_Mice_kidney_NicE-C.hic 4.1 Gb (ftp)(http) HIC
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