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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 21, 2023 |
| Title |
WT A549, MOCK, 2dpi,1 |
| Sample type |
SRA |
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| Source name |
A549
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| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
cell type: lung carcinoma epithelial cells
genotype: WT
treatment: Mock --- 2 dpi
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol phenol chloroform or Qiagen Rneasy kit
Poly-A enrichment and TruSeq stranded OR TruSeq stranded Total RNA with RiboZero Gold
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
TruSeq stranded total RNA, with RiboZero Gold
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| Data processing |
Base calling and sample deconvolution performed via Illumina BaseSpace
Host reads aligned to Homo sapiens HG19 reference genome assembly and quantified using Salmon as made available in Illumina BaseSpace "RNA-Seq Alignment" application
Viral reads were aligned to viral reference genome via Bowtie 2 using custom app on illumina basespace, Integrative Genomics Viewer (IGV) 2.15.2 was then used to generate a .csv files comparing individual base calls per aligned read to each nucleotide in the reference sequence
Assembly: hg19
Supplementary files format and content: .quant.genes.sf Salmon files (show raw and normalized read counts by gene)
Supplementary files format and content: .csv files show the read count for individual base calls compared to the viral reference sequence
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| Submission date |
Mar 17, 2023 |
| Last update date |
Mar 22, 2023 |
| Contact name |
Skyler Andrew Uhl |
| E-mail(s) |
skyleruhl@gmail.com
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| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Microbiology
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| Lab |
Lim & tenOever labs
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| Street address |
1 Gustave L. levy Pl.
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE227592 |
ADAR1 biology can hinder effective antiviral RNA interference |
|
| Relations |
| BioSample |
SAMN33799951 |
| SRA |
SRX19713155 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7103656_SU-13.quant.genes.sf.gz |
401.4 Kb |
(ftp)(http) |
SF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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