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Sample GSM7103656 Query DataSets for GSM7103656
Status Public on Mar 21, 2023
Title WT A549, MOCK, 2dpi,1
Sample type SRA
 
Source name A549
Organism Homo sapiens
Characteristics cell line: A549
cell type: lung carcinoma epithelial cells
genotype: WT
treatment: Mock --- 2 dpi
Extracted molecule total RNA
Extraction protocol Trizol phenol chloroform or Qiagen Rneasy kit
Poly-A enrichment and TruSeq stranded OR TruSeq stranded Total RNA with RiboZero Gold
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description TruSeq stranded total RNA, with RiboZero Gold
Data processing Base calling and sample deconvolution performed via Illumina BaseSpace
Host reads aligned to Homo sapiens HG19 reference genome assembly and quantified using Salmon as made available in Illumina BaseSpace "RNA-Seq Alignment" application
Viral reads were aligned to viral reference genome via Bowtie 2 using custom app on illumina basespace, Integrative Genomics Viewer (IGV) 2.15.2 was then used to generate a .csv files comparing individual base calls per aligned read to each nucleotide in the reference sequence
Assembly: hg19
Supplementary files format and content: .quant.genes.sf Salmon files (show raw and normalized read counts by gene)
Supplementary files format and content: .csv files show the read count for individual base calls compared to the viral reference sequence
 
Submission date Mar 17, 2023
Last update date Mar 22, 2023
Contact name Skyler Andrew Uhl
E-mail(s) skyleruhl@gmail.com
Organization name Icahn School of Medicine at Mount Sinai
Department Microbiology
Lab Lim & tenOever labs
Street address 1 Gustave L. levy Pl.
City New York
State/province New York
ZIP/Postal code 10029
Country USA
 
Platform ID GPL24676
Series (1)
GSE227592 ADAR1 biology can hinder effective antiviral RNA interference
Relations
BioSample SAMN33799951
SRA SRX19713155

Supplementary file Size Download File type/resource
GSM7103656_SU-13.quant.genes.sf.gz 401.4 Kb (ftp)(http) SF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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