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10.1101/gr.268110.120 http://scihub22266oqcxt.onion/10.1101/gr.268110.120 33722935!8015849!33722935     free     free     free Deprecated: Implicit conversion from float 229.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 229.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 229.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       Genome+Res 2021 ; 31 (4): 645-658 Nephropedia Template TP {{tp|p=33722935|t=2021. Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data |pdf=|usr=}}{{33722935}} gab.com Text Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data JO: Genome Res http://www.kidney.de/pget.php?&tw=1&pmid=33722935 #FOAvip We have developed periscope, a tool for the detection and quantification of subgenomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA genome for most open reading frames (ORFs) occurs via RNA intermediates termed "subgenomic RNAs." sgRNAs are produced through discontinuous transcription, which relies on homology between transcription regulatory sequences (TRS-B) upstream of the ORF start codons and that of the TRS-L, which is located in the 5' UTR. TRS-L is immediately preceded by a leader sequence. This leader sequence is therefore found at the 5' end of all sgRNA. We applied periscope to 1155 SARS-CoV-2 genomes from Sheffield, United Kingdom, and validated our findings using orthogonal data sets and in vitro cell systems. By using a simple local alignment to detect reads that contain the leader sequence, we were able to identify and quantify reads arising from canonical and noncanonical sgRNA. We were able to detect all canonical sgRNAs at the expected abundances, with the exception of ORF10. A number of recurrent noncanonical sgRNAs are detected. We show that the results are reproducible using technical replicates and determine the optimum number of reads for sgRNA analysis. In VeroE6 ACE2+/- cell lines, periscope can detect the changes in the kinetics of sgRNA in orthogonal sequencing data sets. Finally, variants found in genomic RNA are transmitted to sgRNAs with high fidelity in most cases. This tool can be applied to all sequenced COVID-19 samples worldwide to provide comprehensive analysis of SARS-CoV-2 sgRNA. Twit Text FOAVip Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data ????Genome Res http://www.kidney.de/pget.php?&tw=1&pmid=33722935 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=33722935 #FOAvip English Wikipedia <ref>{{Cite pmid|33722935}}</ref> Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data #MMPMID33722935 Parker MD; Lindsey BB; Leary S; Gaudieri S; Chopra A; Wyles M; Angyal A; Green LR; Parsons P; Tucker RM; Brown R; Groves D; Johnson K; Carrilero L; Heffer J; Partridge DG; Evans C; Raza M; Keeley AJ; Smith N; Filipe ADS; Shepherd JG; Davis C; Bennett S; Sreenu VB; Kohl A; Aranday-Cortes E; Tong L; Nichols J; Thomson EC; Wang D; Mallal S; de Silva TI Genome Res 2021[Apr]; 31 (4): 645-658 PMID33722935show ga We have developed periscope, a tool for the detection and quantification of subgenomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA genome for most open reading frames (ORFs) occurs via RNA intermediates termed "subgenomic RNAs." sgRNAs are produced through discontinuous transcription, which relies on homology between transcription regulatory sequences (TRS-B) upstream of the ORF start codons and that of the TRS-L, which is located in the 5' UTR. TRS-L is immediately preceded by a leader sequence. This leader sequence is therefore found at the 5' end of all sgRNA. We applied periscope to 1155 SARS-CoV-2 genomes from Sheffield, United Kingdom, and validated our findings using orthogonal data sets and in vitro cell systems. By using a simple local alignment to detect reads that contain the leader sequence, we were able to identify and quantify reads arising from canonical and noncanonical sgRNA. We were able to detect all canonical sgRNAs at the expected abundances, with the exception of ORF10. A number of recurrent noncanonical sgRNAs are detected. We show that the results are reproducible using technical replicates and determine the optimum number of reads for sgRNA analysis. In VeroE6 ACE2+/- cell lines, periscope can detect the changes in the kinetics of sgRNA in orthogonal sequencing data sets. Finally, variants found in genomic RNA are transmitted to sgRNAs with high fidelity in most cases. This tool can be applied to all sequenced COVID-19 samples worldwide to provide comprehensive analysis of SARS-CoV-2 sgRNA. |*Genome, Viral[MESH] |Animals[MESH] |Base Sequence[MESH] |Chlorocebus aethiops[MESH] |Humans[MESH] |Limit of Detection[MESH] |RNA, Viral/*genetics[MESH] |SARS-CoV-2/*genetics[MESH] |Sequence Analysis, RNA/*methods[MESH]Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data (epmc).pdf DeepDyve Pubget Overpricing