EXPERIMENT_TITLE: GSM6777739: RH4_DMSO_24h_HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Bulk RNA is extracted using QIAGEN Rneasy Plus Mini Kit. ChIP samples were fixed with 1% formaldehyde for 15 mins, sonicated, immunoprecipitated using antibody and Dynabeads, washed, eluted, and reverse crosslinked.  ATAC samples were tagmented, PCR amplified, and purified. scRNA-seq samples were processed using the 10x Genomics Chromium Next GEM single cell 3' kit.  Hi-C samples were processed using the Dovetail Micro-C kit. Illumina TruSeq Stranded mRNA and Total RNA library prep, Illumina TruSeq ChIP Library Prep, scRNA-seq using Chromium Next GEM single Cell 3' Reagent kits v3.1, ATAC library from tagmentation and PCR amplification, Hi-C library contructed using Dovetail Micro-C kit
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Fusion-positive alveolar rhabdomyosarcoma (FP-RMS) is an aggressive pediatric sarcoma driven primarily by the PAX3-FOXO1 fusion oncogene, for which therapies targeting PAX3-FOXO1 are lacking. We screened 62,643 compounds using an engineered cell line that monitors PAX3-FOXO1 transcriptional activity identifying a hitherto uncharacterized compound, PFI-63. RNA-seq, ATAC-seq, and docking analyses implicated histone lysine demethylases (KDMs) as its targets. Enzymatic assays confirmed the inhibition of multiple KDMs with highest selectivity for KDM3B. Structural similarity search of PFI-63 identified PFI-90 with improved solubility and potency. Biophysical binding of PFI-90 to KDM3B was demonstrated using NMR and SPR. PFI-90 suppressed the growth of FP-RMS in vitro and in vivo through downregulating PAX3-FOXO1 activity, and combined knockdown of KDM3B and KDM1A phenocopied PFI-90 effects. Thus, we report novel KDM inhibitors with highest specificity for KDM3B. Its potent suppression of PAX3-FOXO1 activity can be exploited as a new therapeutic approach for FP-RMS and other transcriptionally driven cancers. Overall design: RNA-seq, ChIP-seq, ATAC-seq, Hi-C, scRNA-seq.  No replicates.  Drug treatment versus control analysis.
SAMPLE_TITLE: RH4_DMSO_24h_HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "muscle"}, {"TAG": "tissue", "VALUE": "muscle"}, {"TAG": "cell line", "VALUE": "RH4"}, {"TAG": "cell type", "VALUE": "Rhabdomyosarcoma"}, {"TAG": "genotype", "VALUE": "wt"}, {"TAG": "time", "VALUE": "24 hr"}, {"TAG": "treatment", "VALUE": "DMSO"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: RH4_DMSO_24h_HiC
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