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Series GSE164492 Query DataSets for GSE164492
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
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.
 
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.
 
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
Submission date Jan 09, 2021
Last update date May 20, 2021
Contact name Chaitra Rao
E-mail(s) chaitra.rao@unmc.edu
Phone 4025598271
Organization name University of Nebraska Medical Centre
Department Eppley Institute
Lab Robert E Lewis
Street address 505 S 45th St
City Omaha
State/province NE
ZIP/Postal code 68198
Country USA
 
Platforms (1)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (24)
GSM5012128 HCT116 Con Total Rep1
GSM5012129 HCT116 Con Poly Rep1
GSM5012130 HCT116 shKSR1 Total Rep1
Relations
BioProject PRJNA690941
SRA SRP301074

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Supplementary file Size Download File type/resource
GSE164492_HCT116_HCT15_Anota2seq.txt.gz 969.9 Kb (ftp)(http) TXT
GSE164492_HTSeq_gene_counts_matrix.txt.gz 830.1 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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