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| Status |
Public on Apr 23, 2016 |
| Title |
FBXO10 deficiency and BTK activation upregulate BCL2 expression in mantle cell lymphoma |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to identify BTK targets by RNA-seq and high-throughput data analysis and verify these genes by quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods
Methods: mino/z138 sc4/shbtk stable cell lines were generated with tet-on system vector, small hairpins were induced for 48 hours after doxycycline addition, mRNA was exacted and used for RNA sequencing. After TopHat analysis followed by Cufflinks, down/up regulated genes list was generated. qRT–PCR validation was then performed using SYBR Green assays
Results: Using an optimized data analysis workflow and with a fold change ≥1.3 and p value <0.05, thousands of genes were changed. Altered expression of 6 genes was then confirmed with qRT–PCR, demonstrating the high qulity of the RNA-seq method.
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| Overall design |
mino/z138 sc4/shbtk stable cell lines were generated with tet-on system vector, small hairpins were induced for 48 hours after doxycycline addition, total RNA from these cells was then used for RNA-seq analysis.
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| Contributor(s) |
Rui L, Li Y, Lu L |
| Citation(s) |
27157620 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 CA187299 |
Epigenetic Gene Regulation by JAK1 Kinase in Diffuse Large B-Cell Lymphoma |
UNIVERSITY OF WISCONSIN MADISON |
Rui |
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| |
| Submission date |
Apr 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xuehua Zhong |
| Organization name |
Wisconsin Institute for Discovery
|
| Department |
Epigenetics
|
| Street address |
330 N. Orchard St.
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA319310 |
| SRA |
SRP073706 |
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