Gene Expression
Nebulas
Gene Expression NebulasSummary: SARS-CoV-2 is a beta coronavirus causing COVID-19 which first emerged in Wuhan, China and was later declared a pandemic by the World Health Organization. Since then the economical, health and human cost has been enormous for the world. However, little work has been done to understand the transcriptional changes brought about by the virus in human hosts. We have compared COVID-19 positive samples with negative samples from Indian patients to better understand the host response.. We find many genes related to immune response up-regulated in the COVID-19 patients. Many of these are the usual response genes against the viral infection but type I interferon appears to be a key immune response activated against SARS-CoV-2. A large number of the differentially expressed genes were down-regulated pointing towards translational arrest and down regulation of host mRNA during late infection. The down-regulated genes are well correlated with the clinical manifestations and symptoms due to SARS-CoV-2 infection such as the loss of smell and taste. We also find evidence of altered gene expression profiles associated with systemic complications such as neurological disturbances and high insulin requirement. Finally, we have identified many lncRNAs being down-regulated during COVID-19 infections. A few of these lncRNAs have functional role in viral infection. However, to understand the functional role of other lncRNAs, we looked at the function of their closest gene, since lncRNA are believed to have cis functionality. Our analysis suggests a role for lncRNA in down-regulation of metabolic and developmental processes during COVID-19 infection.
Overall Design: Differential expression analysis of RNA-Seq data from COVID-19 positive samples against COVID-19 negative control.
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| Growth Protocol: | - |
| Treatment Protocol: | - |
| Extract Protocol: | Total RNA was extracted from 1ml of VTM using TRIzol reagent (Thermo Fisher Scientific, USA) or TRIzol in combination with Direct-zol RNA Microprep Kits (Zymo, USA) according to the manufacturer’s protocol. RNA was quantified using Qubit RNA HS Assay Kit (Thermo Fisher Scientific, USA) and 1 µg total RNA was used for library preparation. Ribosomal RNA was removed using the RiboCop rRNA Depletion Kit (Lexogen, Austria). |
| Library Construction Protocol: | RNA-Seq libraries were made using the CORALL Total RNA-Seq Library Prep Kit (Lexogen, Austria) according to the manufacturer’s protocol. Briefly, rRNA depleted RNA was reverse transcribed using displacement stop primers which contain partial Illumina-compatible P7 sequences. Linkers containing partial Illumina-compatible P5 sequences and Unique Molecular Identifiers were ligated to the 3’ end of cDNA fragments. The library was PCR amplified to add the remaining adapter sequences and 12 nucleotide unique indices for multiplexing. Samples were sequenced at PE150 using the Illumina NovaSeq 6000. |
| Molecule Type: | rRNA- RNA |
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| Library Layout: | PAIRED |
| Library Strand: | Forward; -; Reverse |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina NovaSeq 6000 |
| Strand-Specific: | Specific; Unspecific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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