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| Status |
Public on Mar 01, 2021 |
| Title |
SOX4 and SMARCA4 cooperatively regulate PI3K signaling through transcriptional activation OF TGFBR2 in triple negative breast cancer |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Genomic and proteomic analyses coupled withmechanistic studies identified TGFBR2as a direct transcriptional target of SOX4and demonstrated that TGFBR2 is required to mediate SOX4-dependent PI3K signaling. We further reportthat SOX4 and the SWI/SNF ATPase SMARCA4, which are uniformly overexpressed in basal-like tumors,form a previously unreported complex that is requiredto maintain an open chromatin conformationat the TGFBR2regulatory regionsin order tomediateTGFBR2expressionand PI3K signaling.
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| Overall design |
Total RNA was extracted from HCC1143 cells treated with either siRNA targeting SOX4 or non-targeting control siRNA for 96 hours. RNA libraries were prepared using theNuGen Ovation Universal RNA-Seq System (Catalog # 0343-32)and paired end (2x48bp) sequencing was performed usingthe Illumina NextSeq system. Paired-end FASTQ files were processed using default parameters of Kallisto version v0.43.1, with 100 bootstraps for the expectation-maximization algorithm. Kallisto transcriptome index was built using the Ensembl human genome reference build 38. Gene level summarization of Kallisto abundance (TPM) was established using the R package Tximport v1.0.3 and R v3.3.1.
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| Contributor(s) |
Mehta GA, Angus SP, Khella CA, Tong K, PVerzi M, Johnson GL, Gatza ML |
| Citation(s) |
33837205 |
| Submission date |
Sep 21, 2020 |
| Last update date |
May 06, 2021 |
| Contact name |
Kevin Tong |
| E-mail(s) |
kevin.tong@hmh-cdi.org
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| Organization name |
Hackensack Meridian Health
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| Department |
CDI
|
| Street address |
111 Ideation Way
|
| City |
Nutley |
| State/province |
NJ |
| ZIP/Postal code |
07110 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA664765 |
| SRA |
SRP284262 |
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