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ChIP-seq analysis of genome-edited MCF7 and T47D ESR1 mutant cell models

ABSTRACT: ChIP-seq analysis of genome-edited MCF7 and T47D ESR1 mutant cell models

PROVIDER: PRJNA515270 | ENA |

REPOSITORIES: ENA

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ChIP-seq analysis of genome-edited MCF7 and T47D ESR1 mutant cell models

Project description:This study is designed to comprehensively characterize the cistromes of Y537S and D538G mutated ER versus WT ER in breast cancer cells. Genome-edited MCF7 and T47D cells were hormone deprived and treated with or without E2 for 45 minuts. Chromatin DNA was then extracted from each sample. The immunoprecipitation was performed using ERα (Santa Cruz Biotechnologies, sc543) antibody. Pooled DNA samples from individual clones were sent to sequencing with Illumina Hiseq 2500 Platform. ChIP-seq reads were aligned to either hg38 genome assembly using Bowtie 2.0, and peaks were called using MACS2.0 with p value below 10E-5. DiffBind was used to perform principle component analysis, identify differentially expressed binding sites and analyze intersection ratios with other data sets. Genomic feature distribution were called using ChIPseeker.

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Project description:FOXA1 ChIP-seq analysis of genome-edited T47D ESR1 mutant cell models

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Project description:Purpose: Transcriptome analysis of ESR1 mutant cells was performed via sequencing total RNA in T47D and MCF7 cell lines containing Y537S and D538G mutations.

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T47D cell line transfected with various ESR1 fusion genes (or with estrogen treatment), vs. YFP transfection alone

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Project description:Affymetrix microarray data was generated from MCF7 breast cancer cells treated in vitro with siRNAs against estrogen receptor alpha (ESR1). Gene expresion of estrogen receptor alpha (ESR1) was knocked down in MCF7 breast cancer cells using siRNA. Then the gene expression profiles of these MCF7 cells, along with non-targetting control treated cells were analysed using Affymetrix Human Genome U133 Plus 2.0 microarrays.

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Heat Shock Factor 1 (HSF1) regulates ESR1 action in breast cancer

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