NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4952820 Query DataSets for GSM4952820
Status Public on Dec 02, 2023
Title Slamseq_Calu3_Covid_24h_Rep3
Sample type SRA
 
Source name Calu3
Organism Homo sapiens
Characteristics agent: SARS-CoV2
time point: 24h
Extracted molecule polyA RNA
Extraction protocol RNA was extracted using Trizol per manufactures protocol, with addition of DTT, and protection from light during the procedure to prevent S-S cross-binding.
5 ug of RNA was used for SLAMseq modifications, as described in Herzog et. al. 2017. Briefly, Iodoacetamide (Sigma I1149) was conjugated to 4SU in a 50mM pH 8.0 phosphate buffer in DMSO/Water (1:1), the reaction was quenched with DTT and RNA was reprecipitated using Ethanol and NaOAc. Libraries were prepared using Quantseq 3’ mRNA-Seq Library Prep Kit (Lexogen).
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Library strategy: Slam-seq
SLAM-seq analysis was done similar to (Muhar et al., Science, 2018). 3'UTR annotations were taken from Gencode annotation release 31 and merged on a gene level. The entire genomic regions of both viruses (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) were added to the human 3’UTR annotations. Adapters and polyA stretches were trimmed from raw reads using fastp (Chen et al., Bioinformatics, 2018). Trimmed reads were further processed with SlamDunk v0.3.4 16 (Neumann et al, BMC Bioinformatics,2018). "Slamdunk all" command was executed with default parameters except '-5 12 -n 100 -t 20 -m -rl 100 --skip-sam'. Differential gene expression was done with DESeq2 (Love et al, Genome Biology, 2014) using raw read counts with at least 2 T>C conversions. Size factors were calculated based on the number of mapped reads (human and viral reads) independent of T>C conversions.
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)
GSE162491 Slam-seq in Calu3 cells upon SARS-CoV2 infection
GSE162495 SARS-CoV2 causes host transcriptional attenuation through an epigenetic pathway.
Relations
BioSample SAMN16979660
SRA SRX9619131

Supplementary file Size Download File type/resource
GSM4952820_Calu3_Covid_24h_Rep3_R1_trimmed.fq_slamdunk_mapped_filtered_tcount.tsv.gz 773.6 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap