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| Status |
Public on May 05, 2023 |
| Title |
Translational fidelity screens reveal eIF3 as a key regulator of start codon selectivity [RNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To investigate the function eIF3D, eIF1A, eIF4G2, and ZNF324 in near-cognate start codon usage, we established K562, HeLa, and Jurkat cell lines in which each target gene has been knocked down by CRISPRi sgRNAs.
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| Overall design |
We then performed RNA-seq in K562 cells depleted of all target genes and RNA-seq in HeLa and Jurkat cells depleted for eIF3D.
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| Contributor(s) |
She R, Weissman JS |
| Citation(s) |
37144468 |
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| Submission date |
Jul 01, 2022 |
| Last update date |
May 05, 2023 |
| Contact name |
Richard She |
| Organization name |
Whitehead Institute
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| Lab |
Weissman Lab
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| Street address |
455 Main St Rm 639, Whitehead Institute
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| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (14)
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| GSM6284625 |
RNA-seq of HeLa cells, Day 5, eIF3D sgRNA |
| GSM6284626 |
RNA-seq of HeLa cells, Day 0, WT |
| GSM6284627 |
RNA-seq of Jurkat cells, Day 5, eIF3D sgRNA |
| GSM6284628 |
RNA-seq of Jurkat cells, Day 0, WT |
| GSM6284629 |
RNA-seq of K562 cells, Day 5, ZNF324 sgRNA |
| GSM6284630 |
RNA-seq of K562 cells, Day 5, eIF1A sgRNA |
| GSM6284631 |
RNA-seq of K562 cells, Day 5, eIF3D sgRNA, replicate 1, batch 2 |
| GSM6284632 |
RNA-seq of K562 cells, Day 5, eIF3D sgRNA, replicate 2, batch 2 |
| GSM6284633 |
RNA-seq of K562 cells, Day 5, eIF3D sgRNA, replicate 3 |
| GSM6284634 |
RNA-seq of K562 cells, Day 5, eIF4G2 sgRNA, replicate 1, batch 2 |
| GSM6284635 |
RNA-seq of K562 cells, Day 5, eIF4G2 sgRNA, replicate 2, batch 2 |
| GSM6284636 |
RNA-seq of K562 cells, Day 0, wild-type replicate 1, batch 2 |
| GSM6284637 |
RNA-seq of K562 cells, Day 0, wild-type replicate 2, batch 2 |
| GSM6284638 |
RNA-seq of K562 cells, Day 0, wild-type replicate 3 |
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| Relations |
| BioProject |
PRJNA854886 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE207330_K562_RNAseq_Table1.txt.gz |
621.7 Kb |
(ftp)(http) |
TXT |
| GSE207330_K562_RNAseq_Table2.txt.gz |
708.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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