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| Status |
Public on Jul 21, 2020 |
| Title |
Cr(VI) Promotes Differential Binding of CTCF to its Cognate Sites |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Using ChIP-seq, we characterize the differential binding of CTCF following 48 hours of low-dose, Cr(VI) treatment. Differentially-bound sites are enriched in regions near genes that are actively transcribed in the basal state and strength of initial binding may be a factor in determining the directionality of binding affinity fluctuations. CTCF and cohesin samples were used to predict intra-TAD chromatin loops in an effort to provide an initial characterization of how Cr(VI) potentially disrupts chromatin-chromatin contacts important for the regulation of transcription, serving as a foundation for future studies.
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| |
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| Overall design |
Examination of CTCF, cohesin, and five histone modifications in control and Cr(VI)-treated (1 µM) Hepa-1c1c7 cells using ChIP-seq.
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| |
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| Contributor(s) |
VonHandorf A, Zablon H, Biesiada J, Medvedovic M, Zhang X, Puga A |
| Citation(s) |
33319643 |
| Submission date |
Jul 14, 2020 |
| Last update date |
Feb 08, 2022 |
| Contact name |
Mario Medvedovic |
| Organization name |
University of Cincinnati
|
| Department |
Department of Environmental Health
|
| Lab |
Laboratory for Statistical Genomics and Systems Biology
|
| Street address |
3223 Eden Av. ML 56
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45267-0056 |
| Country |
USA |
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| Platforms (1) |
| GPL15103 |
Illumina HiSeq 1000 (Mus musculus) |
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| Samples (34)
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| Relations |
| BioProject |
PRJNA646103 |
| SRA |
SRP271747 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE154387_CTCF_processed_data_files.tar.gz |
4.8 Gb |
(ftp)(http) |
TAR |
| GSE154387_H3K27Ac_processed_data_files.tar.gz |
5.1 Gb |
(ftp)(http) |
TAR |
| GSE154387_H3K27me3_processed_data_files.tar.gz |
5.1 Gb |
(ftp)(http) |
TAR |
| GSE154387_H3K36me3_processed_data_files.tar.gz |
4.3 Gb |
(ftp)(http) |
TAR |
| GSE154387_H3K4me3_processed_data_files.tar.gz |
2.6 Gb |
(ftp)(http) |
TAR |
| GSE154387_H3K9me3_processed_data_files.tar.gz |
2.8 Gb |
(ftp)(http) |
TAR |
| GSE154387_Rad21_processed_data_files.tar.gz |
4.3 Gb |
(ftp)(http) |
TAR |
| GSE154387_STAG1_processed_data_files.tar.gz |
3.2 Gb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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