ChIP-seq for RFX1
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ABSTRACT:
PROVIDER: PRJNA866861 | ENA |
REPOSITORIES: ENA
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Project description:Current proteomic approaches disassemble and digest nucleosome particles, blurring readouts of the ‘histone code’. To preserve nucleosome-level information, we developed Nuc-MS, which displays the landscape of histone variants and their post-translational modifications (PTMs) in a single mass spectrum. Combined with immunoprecipitation, Nuc-MS quantified nucleosome co-occupancy of histone H3.3 with variant H2A.Z (sixfold over bulk) and the co-occurrence of oncogenic H3.3K27M with euchromatic marks (for example, a >15-fold enrichment of dimethylated H3K79me2). Nuc-MS is highly concordant with chromatin immunoprecipitation-sequencing (ChIP-seq) and offers a new readout of nucleosome-level biology. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RFX1 in hMDMs cells.
2023-11-08 | GSE210668 | GEO
Project description:We have performed ChIP-sequencing analysis on human FOXN2 and RFX1 target sequences in human embryonic kidney HEK293T cells stably expressing Streptavidin-S-FLAG (SFB) triple-tagged proteins. The NGS sequencing were performed on Illumina MiSeq desktop sequencer.
2015-01-01 | E-MTAB-3120 | biostudies-arrayexpress
Project description:Fusarium graminearum is a major pathogen of Fusarium head blight in wheat, barley, and rice, as well as ear rot and stalk rot in maize. Regulatory Factor X (RFX) transcription factors are well-conserved in animals and fungi, but their functions are diverse, ranging from DNA-damage response to ciliary gene regulation. We investigated the role of the sole RFX transcription factor, RFX1, in F. graminearum. Deletion of rfx1 resulted in multiple defects in hyphal growth, conidiation, virulence, and sexual development. Deletion mutants of rfx1 were more sensitive to various types of DNA damage than the wild-type strain. Septum formation was inhibited and micronuclei were produced in the rfx1 deletion mutants. The results of the neutral comet assay demonstrated that disruption of rfx1 function caused spontaneous DNA double-strand breaks. To understand regulatory mechanisms of rfx1 in F. graminearum, we obtained and analyzed genome-wide transcription profiles generated from the RNA-sequencing data of the wild-type and M-NM-^Trfx1 strains. RNA-sequencing-based transcriptomic analysis revealed that RFX1 suppressed the expression of many genes, including genes for the repair of DNA damage. 2 samples examined: mycelia harvested 24 h after inoculation of wild-type conidia in complete medium; mycelia harvested 32 h after inoculation of M-NM-^Trfx1 conidia in complete medium
2014-01-28 | E-GEOD-52198 | biostudies-arrayexpress
Project description:To investigate the function of RFX1 in the regulation of macrophage polarization, we overexpressed RFX1 in mouse peritoneal macrophages(PMAs) or human CD14+ derived macrophage(hMDMs) by lentivirus infections or reduce RFX1 expression in PMAs from mice with Rfx1 deficiency(CKO) . We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.
2023-11-08 | GSE210667 | GEO
Project description:The aim of the study was to identify RFX1 and RFX2 binding sites in mouse pancreatic beta cells. Chromatin immunoprecipitation experiments were performed with the mouse MIN6 beta cell line and antibodies raised against RFX1 and RFX3. Immunoprecipitated DNA was sequenced using the Genome Analyzer II (Illumina). Antibodies were described in Reith W, Ucla C, Barras E, Gaud A, Durand B, Herrero-Sanchez C, Kobr M, Mach B : RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins. Mol Cell Biol 1994;14:1230–1244
2015-08-22 | E-GEOD-72272 | biostudies-arrayexpress
Project description:Estrogen Receptor alpha (ERα) is a key driver of most breast cancers, and it is the target of endocrine therapies used in the clinic to treat women with ERα positive (ER+) breast cancer. The two methods ChIP-seq (chromatin immunoprecipitation coupled with deep sequencing) and RIME (Rapid Immunoprecipitation of Endogenous Proteins) have greatly improved our understanding of ERα function during breast cancer progression and in response to anti-estrogens. A critical component of both ChIP-seq and RIME protocols is the antibody that is used to pull down the bait protein. To date, most of the ChIP-seq and RIME experiments for the study of ERα have been performed using the sc-543 antibody from Santa Cruz Biotechnology. However, this antibody has been discontinued, thereby severely impacting the study of ERα in normal physiology as well as diseases such as breast cancer and ovarian cancer. Here, we compare the sc-543 antibody with other commercially available antibodies, and we show that 06-935 (EMD Millipore) and ab3575 (Abcam) antibodies can successfully replace the sc-543 antibody for ChIP-seq and RIME experiments.
2019-03-21 | PXD012930 | Pride
Project description:To investigate the function of RFX1 in the regulation of macrophage polarization, we overexpressed RFX1 in mouse peritoneal macrophages(PMAs) by lentivirus infections. We then performed gene expression profiling analysis using data obtained from RNA-seq.
2024-08-06 | GSE236155 | GEO
Project description:Fusarium graminearum is a major pathogen of Fusarium head blight in wheat, barley, and rice, as well as ear rot and stalk rot in maize. Regulatory Factor X (RFX) transcription factors are well-conserved in animals and fungi, but their functions are diverse, ranging from DNA-damage response to ciliary gene regulation. We investigated the role of the sole RFX transcription factor, RFX1, in F. graminearum. Deletion of rfx1 resulted in multiple defects in hyphal growth, conidiation, virulence, and sexual development. Deletion mutants of rfx1 were more sensitive to various types of DNA damage than the wild-type strain. Septum formation was inhibited and micronuclei were produced in the rfx1 deletion mutants. The results of the neutral comet assay demonstrated that disruption of rfx1 function caused spontaneous DNA double-strand breaks. To understand regulatory mechanisms of rfx1 in F. graminearum, we obtained and analyzed genome-wide transcription profiles generated from the RNA-sequencing data of the wild-type and Δrfx1 strains. RNA-sequencing-based transcriptomic analysis revealed that RFX1 suppressed the expression of many genes, including genes for the repair of DNA damage.
2014-01-28 | GSE52198 | GEO
Project description:ChIP-sequencing of Human FOXN2 and RFX1 in HEK293T Cells
| PRJEB7860 | ENA
Project description:RFX1 ChIP-seq on human K562 For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2017-01-04 | GSE92196 | GEO