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| Status |
Public on Oct 25, 2017 |
| Title |
NR4A1 Inhibition Synergizes with Ibrutinib in Killing Mantle Cell Lymphoma Cells |
| 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 NR4A1 targets by RNA-seq and high-throughput data analysis and verify these genes by quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods.
Methods: Jeko/Rec-1 Cas9 control and NR4A1 sgRNA stable cell lines were generated with tet-on system vector, sg RNAs were induced for 48 hours after doxycycline addition, mRNA was extracted 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 |
Jeko/Rec-1 Cas9 control and NR4A1 sgRNA stable cell lines were generated with tet-on system vector, sgRNAs were induced for 48 hours after doxycycline addition, and total RNA from these cells was then used for RNA-seq analysis.
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| |
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| Contributor(s) |
Rui L, Li Y, Lu L |
| Citation(s) |
29167454 |
| |
| Submission date |
Oct 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Lixin Rui |
| E-mail(s) |
lrui@medicine.wisc.edu
|
| Organization name |
Wisconsin Ins for Medical Res
|
| Street address |
1111 Highland ave, Room 4053
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (6)
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| Relations |
| BioProject |
PRJNA415591 |
| SRA |
SRP121232 |
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