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Genome wide SOX4 specific binding sites in BT549 human TNBC cells

ABSTRACT: Genome wide SOX4 specific binding sites in BT549 human TNBC cells

PROVIDER: PRJNA602503 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10919460_1.fastq.gz	Fastqsanger.gz
	SRR10919460_2.fastq.gz	Fastqsanger.gz
	SRR10919461_1.fastq.gz	Fastqsanger.gz
	SRR10919461_2.fastq.gz	Fastqsanger.gz
	SRR10919462_1.fastq.gz	Fastqsanger.gz

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Genome wide SOX4 specific binding sites in BT549 human TNBC cells

Project description:We identified the SOX4 transcription factor and integrin alpha V encoded by the ITGAV gene as important resistance mechanisms to T cell-mediated cytotoxicity of TNBC cells. Here, we performed RNA seq. analysis of SOX4 and ITGAV deficient (CRISPR knockout) BT549 human and 4T1 murine TNBC cells as compared to control edited counterparts. Additionally, we performed SOX4 specific ChIP-seq studies in BT549 human TNBC cells. The objective of the study was to identify the molecular regulators and signaling pathways that mediate resistance to T cell mediated immunity. GSEA analysis of RNA-seq data showed that the 'interferon response' represented one of the top pathways for genes upregulated in SOX4 or ITGAV edited compared to control TNBC cells. In contrast, gene sets associated with TGF beta and TNF alpha/NF kappa b were negatively enriched in both Sox4 and Itgav edited TNBC cells. Further analysis of RNA-seq data showed that SOX4 or ITGAV edited TNBC cells contained higher mRNA levels of many interferon-stimulated genes (ISGs), including genes associated with important innate immune pathways such as RIG-I/MDA-5, cGAS - STING and the AIM2 inflammasome

2021-01-01 | GSE144012 | GEO

RNA-seq analysis of murine Sox4+/+ versus Sox4-/- 4T1 TNBC cells

2021-01-01 | GSE144013 | GEO

miR-200c induction in BT549 TNBC cells

Project description:miR-200c induction in BT549 TNBC cells

| PRJNA423021 | ENA

RNA-seq analysis of murine Sox4+/+ versus Sox4-/- 4T1 TNBC cells

Project description:RNA-seq analysis of murine Sox4+/+ versus Sox4-/- 4T1 TNBC cells

| PRJNA602502 | ENA

SOX4 binding profiling in mouse embryonic neural stem cells (NSCs)

Project description:By chromatin-immunoprecipitating (ChIP) SOX4 in NSCs we identified genome-wide binding sites for SOX4

2018-10-06 | GSE120894 | GEO

Profiling Sox4 binding sites and histone post-translational modifications in adult hepatocytes (CUT&RUN II)

Project description:Recent studies have demonstrated that hepatocytes can be reprogrammed into biliary epithelial cell-like cells. An earlier work in our laboratory nominated Sox4 as an initiation factor of this reprogramming event. To investigate the effect of Sox4 on the change of chromatin landscape of hepatocytes, we exogenosly expressed Sox4 in adult hepatocytes, and profiled its binding sites in a genome wide manner by CUT&RUN-seq. We also profiled histone post-translational modifications of H3K4me1, H3K4me3, H3K27ac and H3K27me3 to explore the influence of Sox4 on the epigenetic landscape of hepatocytes.

2023-11-28 | GSE221224 | GEO

Profiling Sox4 binding sites and histone post-translational modifications in adult hepatocytes (CUT&RUN I)

2023-11-28 | GSE221223 | GEO

miR-200c induction in BT549 TNBC cells

Project description:We performed microarray analysis on BT549 cells that express miR-200c in a doxycycline (dox)-inducible manner from the miR-200c-TripZ system.

2017-12-20 | GSE108271 | GEO

SMAD3 and SOX4 binding profiling in human breast cell lines

Project description:In order to identify genes co-bound by SOX4 and SMAD3 in the context of breast cancer, different breast cell lines (HMLEs, MDA-MB-231 or HCC-1954) were used. Due to low endogenous expression levels for SOX4 in HMLEs in untreated conditions, doxycycline-dependent SOX4 overexpression was obtained by transducing HMLE cells with pIINDUCER21-SOX4 vector..Cells were plated and SOX4 and SMAD3 chromatine-immunoprecipitation was performed in untreated conditions, TGF-beta (2.5ng/ml), doxycycline (0.5ug/ml) or both as indicated. Genome-wide binding sites for SOX4 and SMAD3 was identified in HMLEs, MAD-MB-231 and HCC-1954 cells.

2018-06-11 | GSE104760 | GEO

SOX4 genome binding targets in glioblastoma cell line

Project description:Overexpression of SOX4 in LN229 glioblastoma cells prevents their cell cycle Examination of SOX4 binding profile in prostate cell LN229-SOX4 with LN229-GFP as negative control.

2014-10-20 | E-GEOD-51663 | biostudies-arrayexpress

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