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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 01, 2022 |
| Title |
calu3_000h_cov2_zn101 |
| Sample type |
SRA |
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| Source name |
lung cancer cells – Calu-3
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Calu-3
cell type: lung cancer
treatment: Infected – SARS-CoV-2
hours post-treatment: 0
moi: 0.01
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| Growth protocol |
DMEM + 1% heat inactivated FBS, 100U/mL penicillin, 100 μg/mL streptomycin in 5% CO2 at 37°C
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trypsin-EDTA 0.25% (ThermoFIsher Scientific), then 250 μl Trizol
NEXTFLEX Poly(A) Beads Kit 2.0, then NEXTFLEX Rapid Directional RNA-Seq Kit 2.0 (Perkin Elmer Applied Genomics)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
mRNA (150bp)
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| Data processing |
Reads were mapped against human/African Green Monkey repeat elements in their respective genomes for initial repeat-filtering using Bowtie 2
Repeat-filtered reads were then mapped against their respective STAR indexes (joint hg38-wuhCor1 or chlSab2-wuhCor1) using STAR v2.5.3a "--alignEndsType EndToEnd" option
Gene-level quantification and comparisons using DESeq2
Called peaks in sRNA-seq data mapped to wuhCor1 using Piranha v1.2.1
Quantified unique wuhCor1-mapped sRNA-seq coordinates using in-house python script
Predicted duplexes between host (human or African Green Monkey) transcripts and SARS-CoV-2 sRNAs using RNAhybrid v2.1.2
Genome_build: UCSC (hg18, chlSab2 and wuhCor1)
Supplementary_files_format_and_content: Gene-level counts [mRNA mapping to host quantified with DESeq2 (.csv), sRNA mapping to host quantified with DESeq2 (.csv), sRNA mapping to SARS-CoV-2 quantified with in-house script (.csv)], SARS-CoV-2 sRNA peaks [called with Piranha (.bed)], sRNA Interactions [predicted with RNAhybrid (.csv)]
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| Submission date |
Feb 26, 2022 |
| Last update date |
Mar 01, 2022 |
| Contact name |
Jeremy Sanford |
| E-mail(s) |
jsanfor2@ucsc.edu
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| Phone |
8313345100
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| Organization name |
UC Santa Cruz
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| Department |
Molecular, Cell and Developmental Biology
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| Lab |
Sanford Lab
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| Street address |
1156 High St
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| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE197521 |
SARS-CoV-2 produces a diverse small viral RNA landscape capable of targeting host transcripts |
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| Relations |
| BioSample |
SAMN26279900 |
| SRA |
SRX14302833 |
| 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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