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Series GSE162476 Query DataSets for GSE162476
Status Public on Jan 01, 2023
Title ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [mASPS_ChIP, ASPL_VCP_Pol2]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary ChIPseq experiments identify that ASPSCR1-TFE3 defines active enhancers across the genome and co-distributes with VCP/p97. RNAseq after knock-down of ASPSCR1-TFE3 or VCP, inhibition of VCP, or overexpression of each in alveolar soft part sarcoma cell lines demonstrates their co-dependence. HiChIP defines chromatin conformations that surround ASPSCR1-TFE3 targets and are lost on VCP knock-down.
Overall design ASPS cell lines, tumors from ASPS mouse model and tumors from ASPS patients are used for ChIP-seq with antibodies against ASPSCR1, VCP, POLII and various histone modifications. RNAseq in ASPS cell lines after application of siRNA against control, ASPSCR1-TFE3, or VCP, or application of VCP inhibitor CB-5083. H3K27ac-HiChIP in the FU-UR-1 cell line at baseline and after 6 days of siRNA against VCP.
Contributor(s) Pozner A, Li L, Jones KB
Citation(s) 38326311
Submission date Dec 01, 2020
Last update date Feb 15, 2024
Contact name Jinxiu Li
Organization name China Agricutural University
Department College of biological sciences
Lab State key laboratories of Agrobiotechnology
Street address Yuanmingyuan west road 2#
City Beijing
State/province Beijing
ZIP/Postal code 100193
Country China
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (7)
GSM4952631 mASPS_1_ASPSCR1
GSM4952632 mASPS_1_input
GSM4952633 mASPS_2_ASPSCR1
This SubSeries is part of SuperSeries:
GSE162609 ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP
BioProject PRJNA681928
SRA SRP295437

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Supplementary file Size Download File type/resource
GSE162476_RAW.tar 2.2 Gb (http)(custom) TAR (of BW, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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