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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 02, 2023 |
| Title |
TotalRNAseq_Calu3_Influenza_24h_Rep2 |
| Sample type |
SRA |
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| Source name |
Calu3
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| Organism |
Homo sapiens |
| Characteristics |
agent: Influenza
time point: 24h
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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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) |
| GSE162494 |
Total RNA-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 |
SAMN16979726 |
| SRA |
SRX9619224 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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