|
| Status |
Public on Jan 01, 2023 |
| Title |
ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [Cell_lines_ChIP, FUUR1, 17934_FUUR1_KDs_H3K27ac] |
| Organism |
Homo sapiens |
| 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.
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| 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.
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| |
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| 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) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (32)
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| This SubSeries is part of SuperSeries: |
| GSE162609 |
ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP |
|
| Relations |
| BioProject |
PRJNA681940 |
| SRA |
SRP295446 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE162480_SCR.fragment.bw |
427.4 Mb |
(ftp)(http) |
BW |
| GSE162480_SCR.lambda_control.bw |
927.1 Mb |
(ftp)(http) |
BW |
| GSE162480_TFE30.fragment.bw |
378.4 Mb |
(ftp)(http) |
BW |
| GSE162480_TFE30.lambda_control.bw |
791.0 Mb |
(ftp)(http) |
BW |
| GSE162480_TFE31.fragment.bw |
358.5 Mb |
(ftp)(http) |
BW |
| GSE162480_TFE31.lambda_control.bw |
773.3 Mb |
(ftp)(http) |
BW |
| GSE162480_VCP65.fragment.bw |
360.2 Mb |
(ftp)(http) |
BW |
| GSE162480_VCP65.lambda_control.bw |
765.0 Mb |
(ftp)(http) |
BW |
| GSE162480_VCP67.fragment.bw |
344.6 Mb |
(ftp)(http) |
BW |
| GSE162480_VCP67.lambda_control.bw |
803.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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