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| 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
Other
|
| 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.
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| 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.
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| Web link |
https://www.ncbi.nlm.nih.gov/pubmed/35105668
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| |
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| 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 |
| E-mail(s) |
zhengyuluo@outlook.com
|
| Phone |
18709865282
|
| Organization name |
USTC
|
| Lab |
Song Xiaoyuan Lab
|
| Street address |
Huangshan street
|
| City |
HeFei |
| State/province |
AnHui |
| ZIP/Postal code |
230026 |
| Country |
China |
| |
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| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (32)
|
|
| Relations |
| BioProject |
PRJNA734778 |
| SRA |
SRP322418 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE176066_HeLaS3_NicE-C_100K.bw |
988.3 Mb |
(ftp)(http) |
BW |
| GSE176066_HeLaS3_NicE-C_100K.hic |
4.1 Gb |
(ftp)(http) |
HIC |
| GSE176066_HeLaS3_NicE-C_1M.bw |
1.8 Gb |
(ftp)(http) |
BW |
| GSE176066_HeLaS3_NicE-C_1M.hic |
8.2 Gb |
(ftp)(http) |
HIC |
| GSE176066_HeLaS3_TNFa_NicE-C.bw |
635.6 Mb |
(ftp)(http) |
BW |
| GSE176066_HeLaS3_TNFa_NicE-C.hic |
1.8 Gb |
(ftp)(http) |
HIC |
| GSE176066_HeLaS3_TNFa_RNA-seq.bw |
191.9 Mb |
(ftp)(http) |
BW |
| GSE176066_HeLaS3_control_NicE-C.bw |
639.0 Mb |
(ftp)(http) |
BW |
| GSE176066_HeLaS3_control_NicE-C.hic |
1.9 Gb |
(ftp)(http) |
HIC |
| GSE176066_HeLaS3_control_RNA-seq.bw |
190.0 Mb |
(ftp)(http) |
BW |
| GSE176066_HeLa_Hi-C.hic |
11.6 Gb |
(ftp)(http) |
HIC |
| GSE176066_HeLa_NicE-C.bw |
3.4 Gb |
(ftp)(http) |
BW |
| GSE176066_HeLa_NicE-C.hic |
11.9 Gb |
(ftp)(http) |
HIC |
| GSE176066_HeLa_NicE-seq.bw |
674.3 Mb |
(ftp)(http) |
BW |
| GSE176066_HeLa_RNA-seq.bw |
259.0 Mb |
(ftp)(http) |
BW |
| GSE176066_IMR90_NicE-C.bw |
1.4 Gb |
(ftp)(http) |
BW |
| GSE176066_IMR90_NicE-C.hic |
4.3 Gb |
(ftp)(http) |
HIC |
| GSE176066_Mice_kidney_18m_NicE-C.bw |
2.1 Gb |
(ftp)(http) |
BW |
| GSE176066_Mice_kidney_18m_NicE-C.hic |
15.4 Gb |
(ftp)(http) |
HIC |
| GSE176066_Mice_kidney_18m_RNA-seq.bw |
164.6 Mb |
(ftp)(http) |
BW |
| GSE176066_Mice_kidney_2m_NicE-C.bw |
2.0 Gb |
(ftp)(http) |
BW |
| GSE176066_Mice_kidney_2m_NicE-C.hic |
13.5 Gb |
(ftp)(http) |
HIC |
| GSE176066_Mice_kidney_2m_RNA-seq.bw |
185.2 Mb |
(ftp)(http) |
BW |
| GSE176066_Mice_kidney_NicE-C.bw |
816.7 Mb |
(ftp)(http) |
BW |
| GSE176066_Mice_kidney_NicE-C.hic |
4.1 Gb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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