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| Status |
Public on May 21, 2019 |
| Title |
ARID1A regulates condensin II distribution and chromosomal partition [RNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
ARID1A, a subunit of the switch/sucrose non-fermentable (SWI/SNF) chromatin remodeling complex, influences gene accessibility. However, the role of ARID1A in spatial genomic organization and chromosomal interaction remains elusive. We showed that the SWI/SNF complex interacts with condensin II and they show significant overlapping distributions in enhancers. ARID1A inactivation drives redistribution of condensin II preferentially at enhancers without affecting the interaction between the SWI/SNF and condensing II complexes. ARID1A and condensin II contribute to transcriptionally inactive B compartments, while ARID1A weakens the borders of topologically associated domains. ARID1A inactivation decreases the frequency of genomic interactions over distance, but increases the intermixing of interphase small chromosomes, which was validated by three dimensional chromosome painting. These results demonstrated ARID1A spatially partitions genome and chromosomes.
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| Overall design |
RNA-seq, CHIP-seq and HiC in ARID1A/CAPH2 WT, ARID1A KO and CAPH2 KD cell lines
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| Contributor(s) |
Zhang R, Wu S |
| Citation(s) |
31131328 |
| Submission date |
Sep 17, 2018 |
| Last update date |
Jun 17, 2019 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
priyaw@wistar.org
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| Phone |
2154956837
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| Organization name |
The Wistar Institute
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| Department |
Bioinformatics
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| Lab |
Genomics
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| Street address |
3601 Spruce Street
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (8)
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| GSM3392681 |
RNA-seq in ARID1A WT cells, replicate 1 |
| GSM3392682 |
RNA-seq in ARID1A WT cells, replicate 2 |
| GSM3392683 |
RNA-seq in ARID1A KO cells, replicate 1 |
| GSM3392684 |
RNA-seq in ARID1A KO cells, replicate 2 |
| GSM3392685 |
RNA-seq in CAPH2 WT cells, replicate 1 |
| GSM3392686 |
RNA-seq in CAPH2 WT cells, replicate 2 |
| GSM3392687 |
RNA-seq in CAPH2 KD cells, replicate 1 |
| GSM3392688 |
RNA-seq in CAPH2 KD cells, replicate 2 |
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| This SubSeries is part of SuperSeries: |
| GSE120060 |
ARID1A regulates condensin II distribution and chromosomal partition |
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| Relations |
| BioProject |
PRJNA491603 |
| SRA |
SRP162057 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE120057_ARID1A_RNAseq.txt.gz |
466.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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