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Sample GSM5959187 Query DataSets for GSM5959187
Status Public on Mar 31, 2022
Title Ctrl-1-poly
Sample type SRA
 
Source name BEAS-2B cells
Organism Homo sapiens
Characteristics cell line: BEAS-2B
transient expression: Control
Treatment protocol BEAS-2B cells were nucleofected with the Lonza T1 kit using pcDNA3.4 plasmids expressing ORF9c-3xFLAG, and the empty pcDNA3.4 vector.
Growth protocol Standard cell culture in PneumaCult+supplements media on matrigel coated plates for BEAS-2B cells.
Extracted molecule polyA RNA
Extraction protocol Cells were treated with CHX at 100 µg/ml before fractionation. Total and polysome derived RNA were extracted using Trizol reagent.
Illumina polyA Total RNA kit.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description Ribosome profiling
mRNA from polysome fraction from BEAS-2B cells transiently expressing empty vector rep1
Data processing Library strategy: Ribo-Seq
Raw sequencing reads were trimmed for adapter sequences using cutadapt (v1.14). Trimmed reads were mapped against RepBase (v18.05) to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner (v2.5.2b). Raw read counts were generated from all mapped reads using featureCounts (v1.5.3) package.
Normalized counts were derived from DESeq output.
Assembly: hg19 (GRCh37)
Supplementary files format and content: counts_for_pub.txt contains featureCounts output in comma-delimited format.
Supplementary files format and content: diffexp.tsv files contain DESeq2 output in tab-separated format.
 
Submission date Mar 17, 2022
Last update date Mar 31, 2022
Contact name Gene Yeo
E-mail(s) geneyeo@ucsd.edu
Organization name UCSD
Street address 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL24676
Series (2)
GSE173508 Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins
GSE198899 Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [Ribo-Seq]
Relations
BioSample SAMN26752411
SRA SRX14495056

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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