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| Status |
Public on Jan 01, 2017 |
| Title |
ILF2 Regulates RNA Splicing of DNA Damage Response Genes to Confer Poor Prognosis in 1q21-Amplified Multiple Myeloma |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To understand whether ILF2 is required to ensure the alternative splicing and processing of specific pre-mRNAs in Multiple Myeloma (MM), both in physiological and DNA damage conditions, we performed RNA sequencing (RNA-Seq) analysis of untreated or melphalan-treated ILF2-depleted JJN3 cells. Non-silencing or ILF2 shRNA transduced JJN3 cells were treated with melphalan for 10 hours.
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| Overall design |
Total RNA from untreated or melphalan-treated JJN3 cells transduced with a non-silencing or ILF2 shRNA (two independent replicates per condition) were isolated with the RNeasy Mini kit (Qiagen). Libraries were constructed using the Ovation RNA-Seq System V2 (Nugen) according to the manufacturer’s instructions.
Transcriptomic RNA-Seq was performed on the Illumina HiSeq 2000 platform using the standard paired-end protocol. In total, 60-160 million 76-bp reads were generated per sample. An initial sequence-level quality assessment was performed using FastQC (version 0.10.1, Simon Andrews). The RNA-Seq reads were then mapped to the reference human genome (GRCh37) using Tophat2, allowing a maximum of two mismatches per 76-bp sequencing end. Differential splicing was assessed by multivariate analysis of transcript splicing (MATS) using an FDR<0.05. Pathway enrichment analysis was performed with Pathway Studio.
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| Contributor(s) |
Colla S, Marchesini M, Zhang L |
| Citation(s) |
28669490 |
| |
| Submission date |
Jun 24, 2016 |
| Last update date |
Aug 06, 2019 |
| Contact name |
Li Zhang |
| E-mail(s) |
zhangli271828@gmail.com
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| Organization name |
The University of Texas MD Anderson Cancer Center
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| Department |
Bioinformatics
|
| Street address |
1400 Pressler, unit 1410
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77230 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (8)
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| GSM2213939 |
ILF2 shRNA-transduced JJN3-2 |
| GSM2213940 |
Melphalan-treated non-silencing shRNA-transduced JJN3-1 |
| GSM2213941 |
Melphalan-treated non-silencing shRNA-transduced JJN3-2 |
| GSM2213942 |
Melphalan-treated ILF2 shRNA-transduced JJN3-1 |
| GSM2213943 |
Melphalan-treated ILF2 shRNA-transduced JJN3-2 |
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| Relations |
| BioProject |
PRJNA326776 |
| SRA |
SRP077068 |
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