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Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. (Oh et al. 2016)   (All mRNA-seq Reads tracks)

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     All  All data from Oh et al. 2016   Schema 
     DDX3 R534H total RNAseq  mRNA-seq unique mappers (SRR2096978, SRR2096984) (Oh et al. 2016)   Schema 
     DDX3 R534H total RNAseq with sodium arsenite  mRNA-seq unique mappers (SRR2096981, SRR2096987) (Oh et al. 2016)   Schema 
     DDX3 WT total RNAseq  mRNA-seq unique mappers (SRR2096977, SRR2096983) (Oh et al. 2016)   Schema 
     DDX3 WT total RNAseq with sodium arsenite  mRNA-seq unique mappers (SRR2096980, SRR2096986) (Oh et al. 2016)   Schema 
     Rluc control total RNAseq  mRNA-seq unique mappers (SRR2096976, SRR2096982) (Oh et al. 2016)   Schema 
     Rluc control total RNAseq with sodium arsenite  mRNA-seq unique mappers (SRR2096979, SRR2096985) (Oh et al. 2016)   Schema 
    

Description

Description fromGSE70803: Cells expressing either DDX3 WT or R534H variant were treated with or without sodium arsenite and lysed in the presence of cyclohexime. Total cellular RNAs were extracted and sequenced.

Methods

Raw sequence data were obtainedfrom NCBI FTP directory(SRP060677). Data from the following samples were processed:

DDX3_R534H_total_RNAseq_with_sodium_arsenite mRNA-seq unique mappers Homo sapiens(Oh, et al. 2016)
DDX3_WT_total_RNAseq mRNA-seq unique mappers Homo sapiens(Oh, et al. 2016)
DDX3_WT_total_RNAseq_with_sodium_arsenite mRNA-seq unique mappers Homo sapiens(Oh, et al. 2016)
Rluc_control_total_RNAseq mRNA-seq unique mappers Homo sapiens(Oh, et al. 2016)
Rluc_control_total_RNAseq_with_sodium_arsenite mRNA-seq unique mappers Homo sapiens(Oh, et al. 2016)
DDX3_R534H_total_RNAseq mRNA-seq unique mappers Homo sapiens(Oh, et al. 2016)

Adapter sequence AGATCGGAAGAGCACAC and CAGATCGGAAGAGCACA was removed from reads using Cutadapt An alignment to ribosomal RNA was performed using Bowtie, and aligning reads were discarded. An alignment to the hg38 genome assembly was performed using Bowtie, and reads below 25 nt were discarded. These tracks contain the uniquely mapping reads.,

References

Oh S, Flynn RA, Floor SN, Purzner J, Martin L, Do BT, Schubert S, Vaka D, Morrissy S, Li Y, Kool M, Hovestadt V, Jones DT, Northcott PA, Risch T, Warnatz HJ, Yaspo ML, Adams CM, Leib RD, Breese M, Marra MA, Malkin D, Lichter P, Doudna JA, Pfister SM, Taylor MD, Chang HY, Cho YJ (2016) Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. .Oncotarget. 2016 May 10;7(19):28169-82. doi: 10.18632/oncotarget.8612.