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| Status |
Public on Sep 30, 2020 |
| Title |
Ribosome profiling in DDX3X degron cell lines and covering variants |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
We describe the subset of transcripts that require DDX3 for efficient translation.
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| Overall design |
Ribosome profiling upon auxin-induced degradation of DDX3X, and covered with either wild-type or mutant DDX3X or wild-type DDX3Y was performed from HCT116 cells.
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| Contributor(s) |
Venkataramanan S, Calviello L, Wyler E, Rogowski K, Wilkins K, Tejura M, Thai B, Landthaler M, Floor S |
| Citation(s) |
33905506 |
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| Submission date |
Aug 28, 2020 |
| Last update date |
Jul 24, 2021 |
| Contact name |
Srivats Venkataramanan |
| E-mail(s) |
[email protected]
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| Phone |
4154763275
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| Organization name |
University of California, San Francisco
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| Department |
Cell and Tissue Biology
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| Street address |
513 Parnassus Ave, HSW 740
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| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (16)
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| GSM4751855 |
HCT-116 cells with DDX3X degron, DMSO treated, ribosome profiling, replicate 1 |
| GSM4751856 |
HCT-116 cells with DDX3X degron, DMSO treated, ribosome profiling, replicate 2 |
| GSM4751857 |
HCT-116 cells with DDX3X degron, auxin treated, ribosome profiling, replicate 1 |
| GSM4751858 |
HCT-116 cells with DDX3X degron, auxin treated, ribosome profiling, replicate 2 |
| GSM4751859 |
HCT-116 cells with DDX3X degron, auxin treated, DDX3X WT transfected, ribosome profiling, replicate 1 |
| GSM4751860 |
HCT-116 cells with DDX3X degron, auxin treated, DDX3X WT transfected, ribosome profiling, replicate 2 |
| GSM4751861 |
HCT-116 cells with DDX3X degron, auxin treated, DDX3X R326H transfected, ribosome profiling, replicate 1 |
| GSM4751862 |
HCT-116 cells with DDX3X degron, auxin treated, DDX3X R326H transfected, ribosome profiling, replicate 2 |
| GSM4751865 |
HCT-116 cells with DDX3X degron, DMSO treated, stranded rRNA depleted RNA seq, replicate 1 |
| GSM4751866 |
HCT-116 cells with DDX3X degron, DMSO treated, stranded rRNA depleted RNA seq, replicate 2 |
| GSM4751867 |
HCT-116 cells with DDX3X degron, auxin treated, stranded rRNA depleted RNA seq, replicate 1 |
| GSM4751868 |
HCT-116 cells with DDX3X degron, auxin treated, stranded rRNA depleted RNA seq, replicate 2 |
| GSM4751869 |
HCT-116 cells with DDX3X degron, auxin treated, DDX3X WT transfected, stranded rRNA depleted RNA seq, replicate 1 |
| GSM4751870 |
HCT-116 cells with DDX3X degron, auxin treated, DDX3X WT transfected, stranded rRNA depleted RNA seq, replicate 2 |
| GSM4751871 |
HCT-116 cells with DDX3X degron, auxin treated, DDX3X R326H transfected, stranded rRNA depleted RNA seq, replicate 1 |
| GSM4751872 |
HCT-116 cells with DDX3X degron, auxin treated, DDX3X R326H transfected, stranded rRNA depleted RNA seq, replicate 2 |
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| Relations |
| BioProject |
PRJNA660002 |
| SRA |
SRP279211 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE157063_DE_table_degron.tsv.gz |
1.6 Mb |
(ftp)(http) |
TSV |
| GSE157063_DE_table_mutwt.tsv.gz |
961.4 Kb |
(ftp)(http) |
TSV |
| GSE157063_RAW.tar |
566.8 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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