LitCovid-sentences  

PMC:7366549 / 7902-11439 JSONTXT 9 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T58 0-48 Sentence denotes Sequencing of the positive coronavirus specimens
T59 49-86 Sentence denotes Sanger sequencing of bat coronavirus:
T60 87-181 Sentence denotes The RT-PCR products were separated on 1.5 per cent agarose gel, and 440 bp bands were excised.
T61 182-289 Sentence denotes The excised gels were extracted and purified using a QIAQuick gel extraction kit (Qiagen, Hilden, Germany).
T62 290-505 Sentence denotes The purified products were quantified, and chain-terminated PCR reactions were performed using pathogen-specific forward and reverse primers21 with the BigDye Terminator 3.1 sequencing kit (Applied Biosystems, USA).
T63 506-584 Sentence denotes BigDye reactions were purified using the DyeEx 2.0 spin kit (Qiagen, Germany).
T64 585-722 Sentence denotes The purified chain-terminated reactions were sequenced using the ABI PRISM® 3100 Automated DNA Sequencer (Thermo Fisher Scientific, USA).
T65 723-820 Sentence denotes The sequence data generated were assembled using the Sequencer 5.1 software (Accelrys Inc., USA).
T66 821-873 Sentence denotes Next-generation sequencing (NGS) of bat coronavirus:
T67 874-930 Sentence denotes Selected bat specimens were used for RNA extraction2223.
T68 931-1018 Sentence denotes RNA libraries were prepared and quantified by Qubit® 2.0 Fluorometer (Invitrogen, USA).
T69 1019-1176 Sentence denotes NEB NextrRNA depletion kit (New England Biolabs, USA) was used to remove host ribosomal RNA and re-quantified using Qubit® 2.0 Fluorometer (Invitrogen, USA).
T70 1177-1287 Sentence denotes In brief, the RNA library preparation involved fragmentation, adenylation, adapter ligation and amplification.
T71 1288-1516 Sentence denotes The amplified libraries were quantified using KAPA Library Quantification Kit (KapaBiosystems, Roche, Switzerland) as per the manufacturer's protocol and further loaded onto the Illumina Miniseq NGS platform (Illumina, USA)2223.
T72 1517-1661 Sentence denotes The FASTQ files generated after the completion of the run were analyzed using CLC Genomics Workbench software version 11 (CLC, Qiagen, Germany).
T73 1662-1741 Sentence denotes De novo assembly programme was used to assemble contiguous sequences (contigs).
T74 1742-1864 Sentence denotes The contigs generated were analyzed using BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi) to identify matching sequences.
T75 1865-1979 Sentence denotes The closest matching sequence from GenBank (https://www.ncbi.nlm.nih.gov/genbank/) was used for reference mapping.
T76 1980-2062 Sentence denotes Phylogenetic analysis of partial and complete genome sequences of bat coronavirus:
T77 2063-2295 Sentence denotes The CoV sequences retrieved from RS specimens of Rousettus spp. bats (n=4) were aligned with whole-genome sequences from GenBank using the create alignment function of the CLC genomics workbench (https://digitalinsights.qiagen.com).
T78 2296-2419 Sentence denotes Partial RdRp gene sequences (~419 bp) retrieved by Sanger sequencing, for both the bat species specimens (genomic location:
T79 2420-2529 Sentence denotes 14,701-15,120) were used to construct a phylogenetic tree along with the available RdRp sequences in GenBank.
T80 2530-2730 Sentence denotes Phylogenetic analysis was carried out using the neighbour-joining method available in MEGA v7 software24 using the Kimura 2-parameter nucleotide (nt) substitution model with 1000 bootstrap replicates.
T81 2731-3029 Sentence denotes The nt divergence for the open reading frame (ORF) 1a polyprotein (ORF 1a), ORF 1b polyprotein (ORF 1b), spike protein (S), nucleocapsid phospoprotein (N), envelope protein (E) and membrane glycoprotein (M) genes was estimated using the Kimura 2-parameter model as implemented in the MEGA software.
T82 3030-3146 Sentence denotes The sequences retrieved in the current study, along with those downloaded from GenBank, were grouped into the genus.
T83 3147-3360 Sentence denotes The viruses from the β-CoV genus were further grouped into lineages, L_A, L_B, L_C and L_D, to estimate the evolutionary divergence over the respective gene sequence pairs between groups using the MEGA software24.
T84 3361-3456 Sentence denotes The distance was estimated using a Kimura 2-parameter model with uniform rates among the sites.
T85 3457-3537 Sentence denotes The bootstrap of 500 replicates was used to estimate the variation in the model.