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Sample GSM4952914 Query DataSets for GSM4952914
Status Public on Dec 02, 2023
Title TotalRNAseq_Calu3_Mock_24h_Rep1
Sample type SRA
 
Source name Calu3
Organism Homo sapiens
Characteristics agent: Mock
time point: 24h
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol (R2050; Zymo Research, USA), as per manufacturer’s instructions. Followed by purification using RNA Clean & Concentrator (R1017; Zymo esearch, USA) and DNase I Set (E1010; Zymo Research, USA), as per manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing RNA-seq data was analyzed using the RNA-seq module from the snakePipes package (Bhardwaj et al, Bioinformatics, 2019). A hybrid genome of human (genome build hg38, Gencode release 31) and viral genomes ( H1N1: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=370129 and SARS_Cov-2: https://www.ncbi.nlm.nih.gov/nuccore/1798174254) was used as reference for mapping and read counting. Differential gene expression analysis was done using DESeq2 (Love et al, Genome Biology, 2014), using the total number of mapped human and viral reads to calculate size factors.
Genome_build: hg38
Supplementary_files_format_and_content: Table in tsv format with raw counts
 
Submission date Dec 02, 2020
Last update date Dec 02, 2023
Contact name Barbara Hummel
Organization name Max Planck Institute of Immunobiology and Epigenetics
Street address Stübeweg 51
City Freiburg
ZIP/Postal code 79108
Country Germany
 
Platform ID GPL24676
Series (2)
GSE162494 Total RNA-seq in Calu3 cells upon SARS-CoV2 infection
GSE162495 SARS-CoV2 causes host transcriptional attenuation through an epigenetic pathway.
Relations
BioSample SAMN16979721
SRA SRX9619229

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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