LitCovid-sentences  

PMC:7354481 / 13096-15193 JSONTXT 9 Projects

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Id Subject Object Predicate Lexical cue
T89 0-230 Sentence denotes Bioproject data was obtained from PRJNA615032 bioproject trancriptome data, which includes lung biopsies from SARS-CoV-2-infected patients and healthy volunteers as well as mock and SARS-CoV-2-transfected NHEB and A549 cell lines.
T90 231-389 Sentence denotes The data have been deposited with links to BioProject accession number PRJNA615032 in the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/).
T91 390-466 Sentence denotes All the selected data were reanalysed at the Rosalind bioinformatics server.
T92 467-651 Sentence denotes Data analysis was performed according to 1.5 fold change between untransfected and transfected cell lines in a data pool calculation for both cell lines at p < 0.05 significance level.
T93 652-807 Sentence denotes Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA, USA).
T94 808-847 Sentence denotes Reads were trimmed using cutadapt [25].
T95 848-895 Sentence denotes Quality scores were assessed using FastQC [26].
T96 896-974 Sentence denotes Reads were aligned to the Homo sapiens genome built by GRCh38 using STAR [27].
T97 975-1109 Sentence denotes Individual sample reads were quantified using HTseq [28] and normalized via relative log expression (RLE) using DESeq2 R library [29].
T98 1110-1250 Sentence denotes Read distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC [30].
T99 1251-1353 Sentence denotes DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction.
T100 1354-1571 Sentence denotes Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (partitioning around medoids) method using the fpc R library (https://cran.r-project.org/web/packages/fpc/index.html).
T101 1572-1702 Sentence denotes Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies.
T102 1703-1848 Sentence denotes The topGO R library [31], was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction.
T103 1849-2004 Sentence denotes Several database sources were referenced for enrichment analysis, including Interpro [32], NCBI [33], MSigDB [34,35], REACTOME [36], and WikiPathways [37].
T104 2005-2097 Sentence denotes Enrichment was calculated relative to a set of background genes relevant for the experiment.