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SRX9813091: GSM5012128: HCT116 Con Total Rep1; Homo sapiens; RNA-Seq
1 ILLUMINA (NextSeq 550) run: 50.2M spots, 3.8G bases, 1.3Gb downloads

Submitted by: NCBI (GEO)
Study: Next generation sequencing analysis of control and KSR1 knockdown CRC cell line translatomes.
show Abstracthide Abstract
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.
Sample: HCT116 Con Total Rep1
SAMN17268940 • SRS7997101 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: NextSeq 550
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: The total RNA and RNA pooled from the polysome fraction (fractions 6-9) was isolated using RNAzol. RNA sequencing libraries were prepared using 500 ng of RNA using Truseq mRNA protocol kit (Illumina) RNA libraries were prepared for sequencing using standard Illumina protocols
Experiment attributes:
GEO Accession: GSM5012128
Links:
Runs: 1 run, 50.2M spots, 3.8G bases, 1.3Gb
Run# of Spots# of BasesSizePublished
SRR1339396350,228,6593.8G1.3Gb2021-01-11

ID:
12852808

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