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| Status |
Public on Mar 20, 2019 |
| Title |
Gene Expression Profiling of WT and KDM3A Knocked out Cell |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulator for hippo target genes. We found that H3K27ac upregulation is highly correlated with gene activation, but not H3K4me3; and transcription repression of certain TEAD1 target genes, such as BBC3, is important for the pathway function. KDM3A knockout caused upregulation of H3K9me2 mainly on TEAD1-binding enhancers rather than gene bodies, leading to decrease of H3K27ac and TEAD1 binding on enhancers and impaired transcription.
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| Overall design |
KDM3A was knocked out in HCT116 and the gene expression profile was studied by RNA sequencing
Please note that, in the sample titles, M represents Mock, which means cell cultureed in normal state. S represents Starvation, which mens cells growed up in normal culture in a due time, then change the nomal culture into no-serum culture. S+F means addition of FBS into the no-serum culture after cell-starved for for 24 hours.
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| |
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| Contributor(s) |
Wang H, Long Q |
| Citation(s) |
30649550 |
| Submission date |
Jan 09, 2018 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Pin-Ji Lei |
| E-mail(s) |
leipinji@gmail.com
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Department of Radiation Oncology
|
| Lab |
Edwin L. Steele Laboratories
|
| Street address |
100 Blossom Street
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE108922 |
Genome-wide maps of chromatin state and Gene Expression Profiling in HCT116 cells |
|
| Relations |
| BioProject |
PRJNA429182 |
| SRA |
SRP128505 |
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