|
| Status |
Public on Feb 02, 2021 |
| Title |
mock-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Caco-2
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cell line
cell line: Caco-2
infection status: none
clofazimine treatment: mock
|
| Treatment protocol |
For the experiment on Caco-2 cells, cells were infected with/without SARS-CoV-2 virus at MOI=4 for 1 hour, followed by incubation with fresh medium with 10uM clofazimine or DMSO control. After 3 or 6 hours, cells were collected for RNA extraction. For the experiment on golden hamsters, we delivered clofazimine through oral route utilizing corn oil as vehicle. An equivalent hamster dose of 25 mg/kg/day was converted based on body surface area. Prophylactic treatment through oral administration of clofazimine was given at -3, -2 and -1 dpi (25 mg/kg/day), followed by virus challenge at 0dpi through intranasal route (10^5 PFU/hamster); therapeutic post-exposure administration of clofazimine was performed at 1, 2, and 3 dpi applying the same drug dosage and virus inoculum. Lung tissues were collected at 4dpi for prophylactic and therapeutic groups. For uninfected group, clofazimine was given for 3 consecutive days and lung tissues were collected on day 4.
|
| Growth protocol |
Caco-2 cells were maintained in DMEM culture medium supplemented with 20% heat-inactivated FBS, 50 U/ml penicillin and 50 µg/ml streptomycin
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Qiagen RNeasy Mini Kit
cDNA libraries were prepared by KAPA mRNA HyperPrep Kit.1 ug of total RNA was used as starting material. Manufacturer’s protocol was followed.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CFZ_SARS2_rpkm.csv
mock-1
|
| Data processing |
Fastq files from RNA-seq were quality examined by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were processed by cutadapt to remove reads with low quality and to trim adapters.
Trimmed reads were aligned to hg38 reference genome using Tophat2
Reads assigned to each gene were counted by featureCounts with refseq gene sets as references.
Genes without at least 1 read mapped on average in each sample were considered undetectable and were filtered out. Read counts were normalized by Trimmed Mean of M-values (TMM) method and RPKM of each gene was calculated using R package edgeR
Genome_build: hg38 for Caco-2 cells; MesAur1.0 for hamster lung tissues
Supplementary_files_format_and_content: CSV files include RPKM values for each sample
|
| |
|
| Submission date |
Dec 08, 2020 |
| Last update date |
Feb 02, 2021 |
| Contact name |
Xiangzhi Meng |
| E-mail(s) |
mengxiangzhi919@gmail.com
|
| Organization name |
The University of Hong Kong
|
| Street address |
21 Sassoon Road
|
| City |
Hong Kong SAR |
| ZIP/Postal code |
000000 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE162899 |
Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters |
|
| Relations |
| BioSample |
SAMN17035227 |
| SRA |
SRX9654044 |
