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Hypoxia-related Transcription factor ChIP-Seq data in T47D breast cancer cells

ABSTRACT: We report the comprehensive genome-wide binding peaks for key factors inovled in oxygen sensing pathways, such as HIF1α, HIF1β and EglN2. In addition, we also report the genome-wide binding peaks for NRF1 in breast cancer cells We conducted HA-EglN2, HIF1α, HIF1β (ARNT) or NRF1 ChIP-Seq in the T47D cell line that overexpresses HA-EglN2 in the presence of hypoxia (1%) and DMOG treatment. T47D parental cells treated with the same condition followed by HA ChIP-seq served as the control to filter non-specific binding.

ORGANISM(S): Homo sapiens

SUBMITTER: Qing Zhang

PROVIDER: E-GEOD-59935 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:We report the comprehensive genome-wide binding peaks for key factors inovled in oxygen sensing pathways, such as HIF1α, HIF1β and EglN2. In addition, we also report the genome-wide binding peaks for NRF1 in breast cancer cells

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HNF4α and TCF4 (TCF7L2) ChIPseq in Tet-On HCT116 inducible cell lines that express either the human HNF4α2 or HNF4α8 under the control of doxycycline (DOX) [ChIP-Seq]

Project description:Purpose: Aim of the study is to determine how many of the dysregulated genes in the RNAseq are direct targets of (P1) HNF4α2 and (P2) HNF4α8 and examine HNF4α and TCF4 binding in vivo. We performed ChIPseq on TCF4 in the absense or presence of DOX in the Tet-On inducible HCT116 HNF4α2 and HNF4α8 lines, and ChIPseq for HNF4α (a445 Ab) in the presence of DOX. Methods: HNF4α2 and HNF4α8 lines were induced with 0.3 μg/mL DOX for 24 hours. Samples were generated by deep sequencing, using the NEXTflex ChIPseq. Result: There were more HNF4α2 peaks than HNF4α8 peaks, with some common peaks bound by HNF4α2 and HNF4α8. Binding patterns were observed between HNF4α and TCF4. Conclusion: HNF4α2 can displace TCF4 better than HNF4α8 on AP-1 bound sites. Tet-On inducible HCT116 cell (HNF4α2 and HNF4α8) lines, treated with (0.3 μg/mL) or without DOX for 24 hours, were 50bp single-end sequenced using Illumina-compatible-NEXTflex ChIP kit (Bioo Scientific).

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Genome-wide chromatin binding of transcription factor E2F1 in castration resistant prostate cancer (CRPC) cells

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ChIP-seq of H3-K4me3 from WI-38hTERT/sh3-H2AFJ and WI-38hTERT/sh-NT fibroblasts in proliferation and etoposide-induced senescence.

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2015-06-25 | E-GEOD-62666 | biostudies-arrayexpress

Expression data with either EglN2 or control knockdown in T47D cells

Project description:In order to perform integrated analysis for EglN2 ChIP-Seq and microarray to identify EglN2 direct target genes, we performed the microarray analysis for T47D breast cancer cells with either control or EglN2 siRNA followed by hypoxia+DMOG treatment T47D cells were transfected with either control or EglN2 siRNA in duplicate with RNAi max. 36 hours following transfection, cells were treated with hypoxia (1%) and DMOG (1 mM) for 16 hours. Following treatment, total RNA was extracted using Rnaeasy kit from Qiagen.

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2020-10-23 | E-MTAB-9335 | biostudies-arrayexpress

Expression data with either EglN2 or control knockdown in T47D cells

2014-07-31 | GSE59936 | GEO

Methylated RNA immunoprecipitation sequencing in the Kasumi-1 cell line treated with CoCl2 and echinomycin

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