Characterization of chromatin accessibility through the DNaseI hypersensitivity assay in breast cancer cells treated with either Dex or E2

UID: 10772

Author(s): Swinstead, Erin E., Baek, Songjoon, Hager, Gordon L

Description: Summary from the GEO: "The estrogen receptor (ER), glucocorticoid receptor (GR), and forkhead box protein 1 (FoxA1) are significant factors in breast cancer progression. FoxA1 is well-established as a pioneer factor for steroid receptor recruitment to chromatin. Here we show that ER and GR have the ability to alter the genomic response of FoxA1 to specific binding sites within the genome. These findings alter the classical understood mechanism of FoxA1 establishing a dynamic transcription factor that can be regulated by hormones."

Overall Design from the GEO: "We examined the ER and GR mediated affects on FoxA1 binding patterms"

Subject of Study

Subject(s)

OncoTree Cancer Type(s)

Breast

Access via GEO
BEDGRAPH and CSV files of genome binding/occupancy profiling by high throughput sequencing
Accession #: GSE72250

Access via SRA
DNase Seq of 12 Samples
Accession #: SRP062678

Access via BioProject
Additional information about the overall inititative.
Accession #: PRJNA293470
Access Restrictions: Free to All
Access Instructions: The NCBI Gene Expression Omnibus, SRA and BioProject databases provide open access to these files. SRA and/or tar files can be downloaded directly from the site or viewed in the NCBI SRA Run Selector (link at bottom of page).
Associated Publications: Li F, Han M, Dai P, et al. Distinct mechanisms for TMPRSS2 expression explain organ-specific inhibition of SARS-CoV-2 infection by enzalutamide. Nature Communications. 2021; 12:866.

Swinstead EE, Miranda TB, Paakinaho V, et al. Steroid Receptors Reprogram FoxA1 Occupancy through Dynamic Chromatin Transitions. Cell. 2016;165(3):593-605.
Data Type: Genomic
Equipment Used: Illumina NextSeq 500
Software Used: SRA Toolkit
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
Dataset Format(s): CSV, SRA, BEDGRAPH
Data Tool(s): DNase Sequencing
Dataset Size: 1.4 GB (TAR of BEDGRAPH), 13.6 MB (CSV), 7.1 GB (SRA)

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