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| Status |
Public on Dec 02, 2023 |
| Title |
Slamseq_Calu3_Covid_6h_Rep3 |
| Sample type |
SRA |
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| Source name |
Calu3
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| Organism |
Homo sapiens |
| Characteristics |
agent: SARS-CoV2
time point: 6h
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| 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).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Dec 02, 2020 |
| Last update date |
Dec 02, 2023 |
| Contact name |
Barbara Hummel |
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
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| Street address |
Stübeweg 51
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| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
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| 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. |
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| Relations |
| BioSample |
SAMN16979657 |
| SRA |
SRX9619134 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4952823_Calu3_Covid_6h_Rep3_R1_trimmed.fq_slamdunk_mapped_filtered_tcount.tsv.gz |
826.7 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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