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| Status |
Public on Oct 01, 2023 |
| Title |
SARS CoV-2 Vero E6 infected samples at 16 hours rep2 |
| Sample type |
SRA |
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| Source name |
Vero E6 cells
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| Organism |
Chlorocebus sabaeus |
| Characteristics |
cell type: Vero E6 cells
treatment: SARS-CoV-2/human/USA/UF-13/2020 (GenBank: MT620766.1)
time point: 16 hrs
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were resuspended in 1mL Trizol, 200 µL chloroform was added to each sample, and samples were mixed thoroughly by vortexing, then incubated at room temperature for 3 minutes. Samples were centrifuged at 12,000xg for 15 minutes at 4°C. The upper aqueous layer was transferred to a new tube and 500 µL isopropanol was added and mixed by vortex-ing, prior to incubation at room temperature for 10 minutes. RNA was pelleted by centrifuging at 12,000 xg for 10 minutes at 4°C, and supernatant was discarded. The pellet was rinsed in 75% ethanol and pelleted by centrifuging at 7,500xg for 5 minutes at 4°C. Ethanol wash and spin were repeated a second time. The pellet was air dried in an inverted tube. Genomic DNA was digested using the TURBO DNA-free™ Kit (Invitrogen #AM1907) according to manufac-turer instructions. Samples were mixed with 350 µL buffer RLT from the RNeasy® Mini kit (Qi-agen #74104) and 250 µL 100% ethanol, then transferred to a RNeasy® Mini kit spin column. Columns were centrifuged at 8,000xg for 15 seconds at room temperature, and flow-through was discarded. Buffer RPE (500 µL) was added to the column, which was centrifuged at the same conditions, and flow-through was discarded. The RPE wash was repeated a second time. The column was transferred to a fresh collection tube and centrifuged at 12,000 xg for 1 min to dry. RNA was eluted by adding 50 µL of nuclease free water and centrifuging for 1 mi-nute at 8,000xg.
RNA libraries were prepared for sequencing using standard Illumina protocols
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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 |
Sequenced reads were trimmed for adaptor sequences, <20 nucleotide reads and low-quality reads. RNA STAR v2.7.7a was used to map samples to the Chlorocebus sabaeus genome and associated annotation (GenBank accession # GCA_015252025.1). feature-Counts v 2.0.1 was used to sum reads for each gene. Read counts for each sample were input into DESeq2 v 1.22.1 to call differential gene ex-pression, analyzing the effect of time, drug, and virus on the samples.
Genome_build: GenBank accession # GCA_015252025.1
Supplementary_files_format_and_content: tab-delimited text files including read counts for each gene
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| Submission date |
Jun 14, 2021 |
| Last update date |
Oct 01, 2023 |
| Contact name |
Rhoel Dinglasan |
| E-mail(s) |
rdinglasan@epi.ufl.edu
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| Organization name |
University of Florida
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| Street address |
2055 Mowry Rd
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| City |
Gainesville |
| State/province |
Florida |
| ZIP/Postal code |
32601 |
| Country |
USA |
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| Platform ID |
GPL28895 |
| Series (1) |
| GSE178157 |
Niclosamide as a chemical probe for analyzing SARS-CoV-2 modulation of host cell lipid metabolism |
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| Relations |
| BioSample |
SAMN19696878 |
| SRA |
SRX11141005 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5381097_xV16_2_Counts.tab.gz |
140.1 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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