|
| Status |
Public on Aug 23, 2022 |
| Title |
Caco2 cells 48h Mock-3 |
| Sample type |
SRA |
| |
|
| Source name |
Caco2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Caco2
cell type: Colorectal adenocarcinoma cells
infection: Uninfected
cov-2 variant: None
time point: 48h
|
| Treatment protocol |
1 MOI infection for three time points 24, 48, and 72 Hours.
|
| Growth protocol |
Caco2 cells were cultured in cDMEM supplemented with 20% FBS and 1× penicillin-streptomycin cocktail (Gibco) at 37°C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cellular RNA prepared using MN nucleospin RNA isolation kit (Takara).
Library preparation was done using the MGIEasy RNA Library Prep Set (MGI) according to the manufacturer’s instructions. In brief, 500 ng total RNA was used as starting material and ribosomal RNA was removed using Ribo-Zero Plus rRNA Depletion Kit (Illumina). The rRNA depleted samples were fragmented, reverse transcribed and second strand was synthesised. DNA was then purified using DNA Clean Beads provide in the kit followed by end repair and A-tailing. Barcoding and adaptor ligation was performed and the samples were purified. Samples were amplified using adaptor specific primers and quantified using Qubit dsDNA high sensitivity kit (ThermoScientific). Sample fragment size was determined using 4200 TapeStation (Agilent). The samples were denatured and single stranded circular DNA strands were created. Rolling cycle amplification was performed and DNA nanoballs were created. The samples were loaded onto FCL and sequenced at PE100.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
HHK-15
Cellular RNA
|
| Data processing |
MGI adapters and low-quality reads were removed from raw sequencing reads using cutadapt. Reads with quality scores less than 20 and smaller than 36 bp were discarded. The processed reads were then mapped to the human genome GRCh38 using hisat2 with default parameters. Uniquely aligned reads were counted using featureCounts of Subread package. There were 60683 genes in the gtf file, downloaded from ensembl, for which we had count information. Genes with total read count 10 across all the samples were removed resulting in 35906 genes for further analysis. Differential gene expression analysis was performed using DESeq2. Genes with adjusted p-value < 0.05 and absolute log2 Fold change > 1 were considered differentially expressed. For PCA plot and heat map, the raw read counts were rlog normalized, available with the DESeq2 package.
Genome_build: Human GRCh38
Supplementary_files_format_and_content: countMatrix_unstranded_upload.count.txt: Tab-delimited counts file.
|
| |
|
| Submission date |
Jan 05, 2022 |
| Last update date |
Aug 23, 2022 |
| Contact name |
Nitesh Kumar Singh |
| E-mail(s) |
[email protected]
|
| Organization name |
Center for Cellular and Molecular Biology
|
| Department |
Bioinformatics
|
| Street address |
Habsiguda
|
| City |
Hyderabad |
| State/province |
Telangana |
| ZIP/Postal code |
500007 |
| Country |
India |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE193122 |
SARS-CoV-2 Variant Delta Potently Suppresses Innate Immune Response and Evades Interferon-Activated Antiviral Responses in Human Colon Epithelial Cells |
|
| Relations |
| BioSample |
SAMN24662046 |
| SRA |
SRX13627426 |
