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DNA accessibility sites requiring SMARCA4 activity in neuroblastoma cells [ATAC-seq]

ABSTRACT: To reveal the genome-wide targets of SWI/SNF complexes in neuroblastoma cells, we performed ATAC-seq in IMR-32 cells with or without SMARCA4 inactivation. To identify changes in DNA accessibility following SMARCA4 inactivation, we used either the small-molecule catalytic inhibitor BRM014, auxin-induced degradation of IMR-32 cells engineered with SMARCA4 tagged to the minimal auxin-induced degron (SMARCA4-mAID), or the corresponding vehicle controls. Analysis of these locations reveal that SMARCA4-dependent sites are located at enhancers used by the neuroblastoma core regulatory circuitry.

ORGANISM(S): Homo sapiens

PROVIDER: GSE190706 | GEO | 2023/10/24

REPOSITORIES: GEO

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Transcriptional effects of SMARCA4 inhibition on neuroblastoma cells [4sU RNA-seq]

Project description:To reveal fast-acting transcriptional effects of SWI/SNF inhibition in neuroblastoma cells, we performed 4sU metabolic labeling followed by RNA-seq in IMR-32, KELLY, and SK-N-DZ cells and compared the effects of BRM014 with DMSO vehicle control. We also compared these effects to auxin-induced degradation of SMARCA4 in engineered cells with the minimal auxin-induced degron (SMARCA4-mAID). Analysis of transcripts reveal that SMARCA4 inhibition leads to suppression of transcripts involved in the G1 checkpoint.

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Project description:To reveal the genome-wide targets of SWI/SNF complexes in neuroblastoma cells, we performed ChIP-seq of SMARCA4 (BRG1) in IMR-32, KELLY, and SK-N-DZ cells. We used these libraries to examine chromatin occupancy profiling. Analysis of locations reveal that SMARCA4 targets directly regulate sites regulated by the neuroblastoma core regulatory circuitry.

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Chromatin profiling following SWI/SNF inhibition in neuroblastoma cells [ChIP-seq]

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Transcription factor activating protein 2 beta (TFAP2B) mediates noradrenergic neuronal differentiation in neuroblastoma

Project description:Single-color gene expression profiles from IMR-32 neuroblastoma cell lines were generated using 44K oligonucleotide microarrays. To gain insights into the molecular processes occurring upon TFAP2B re-expression, we performed gene expression measurements in TFAP2B and GFP expressing transgenic IMR-32 neuroblastoma cell lines at d2 and d7 of transgene induction. Single-color gene expression profiles from IMR-32 neuroblastoma cell lines were generated using 44K oligonucleotide microarrays. Total RNA of TFAP2B- and GFP-expressing IMR-32 cells was isolated at day 2 and day 7 using Trizol.

2015-10-27 | E-GEOD-74350 | biostudies-arrayexpress

Transcription factor activating protein 2 beta (TFAP2B) mediates noradrenergic neuronal differentiation in neuroblastoma

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Temporal Quantitative Phosphoproteomic Profiling of SH-SY5Y and IMR-32 Neuroblastoma Cells During All-trans Retinoic Acid-Induced Neuronal Differentiation

Project description:The human neuroblastoma cell lines SH-SY5Y and IMR-32 can be differentiated into neuron-like phenotypes through treatment with all-trans retinoic acid (ATRA). After differentiation, these cell lines are extensively utilized as in vitro models to study various aspects of neuronal cell biology. However, temporal and quantitative profiling of the proteome and phosphoproteome of SH-SY5Y and IMR-32 cells throughout ATRA-induced differentiation has been limited. Here, we performed relative quantification of the phosphoproteomes of SH-SY5Y and IMR-32 cells at multiple time points during ATRA-induced differentiation. The data presented serve as a valuable resource for investigating temporal protein and phosphoprotein abundance changes in SH-SY5Y and IMR-32 cells during ATRA-induced differentiation.

2024-01-24 | PXD046871 | Pride

Temporal Quantitative Proteomic Profiling of SH-SY5Y and IMR-32 Neuroblastoma Cells During All-trans Retinoic Acid-Induced Neuronal Differentiation

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2024-01-24 | PXD046900 | Pride

Homo sapiens

Project description:RNAseq in IMR-32 neuroblastoma cells

| PRJNA232668 | ENA

ATAC-seq in neuroblastoma IMR-32 cell line

Project description:ATAC-seq to define open chromatin in the neuroblastoma IMR-32 cell line.

2018-08-16 | E-MTAB-6562 | biostudies-arrayexpress

DNA accessibility sites requiring SWI/SNF activity in AML [ATAC-seq]

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2023-01-10 | GSE190721 | GEO

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