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Status |
Public on Jan 10, 2021 |
Title |
Next generation sequencing analysis of control and KSR1 knockdown CRC cell line translatomes. |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
KSR1 signaling alters the translational landscape of human CRC cells to support their survival. To determine the effect of KSR1 on translatomes in colon cancer cells, we performed genome-wide polysome profiling. We stably expressed short hairpin RNA (shRNA) constructs targeting KSR1 or a non-targeting control in two K-Ras mutant CRC cell lines, HCT116 and HCT15. We isolated and quantified both total mRNA and efficiently translated mRNAs (associated with ≥ 3 ribosomes) using RNA sequencing. We used Anota2seq to calculate translation efficiency (TE) by comparing the differences in efficiently translated mRNAs to the total transcript of each mRNA.
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Overall design |
HCT116 and HCT15 control and KSR1 knockdown cells, total RNA and polysomal RNA was extracted using sucrose gradient fraction from three independent experiments for each condition.
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Contributor(s) |
Lewis RE, Rao C, Southekal S |
Citation(s) |
33970103 |
NIH grant(s) |
Grant ID |
Grant title |
Affiliation |
Name |
P20 GM121316 |
Nebraska Center for Molecular Target Discovery and Development |
UNIVERSITY OF NEBRASKA MEDICAL CENTER |
Robert E. Lewis |
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Submission date |
Jan 09, 2021 |
Last update date |
May 20, 2021 |
Contact name |
Chaitra Rao |
E-mail(s) |
chaitra.rao@unmc.edu
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Phone |
4025598271
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Organization name |
University of Nebraska Medical Centre
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Department |
Eppley Institute
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Lab |
Robert E Lewis
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Street address |
505 S 45th St
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City |
Omaha |
State/province |
NE |
ZIP/Postal code |
68198 |
Country |
USA |
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Platforms (1) |
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Samples (24)
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Relations |
BioProject |
PRJNA690941 |
SRA |
SRP301074 |