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Novaseq sp lane

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The NovaSeq SP lane is a component of the NovaSeq 6000 Sequencing System, a high-throughput next-generation sequencing platform developed by Illumina. The NovaSeq SP lane is designed to perform sequencing runs on flow cells, which are the primary sample-containing cartridges used in the NovaSeq 6000 system.

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Lab products found in correlation

Superscript 4 first strand synthesis kit, by Thermo Fisher Scientific (3 mentions) Swift snap amplicon sars cov2 kit, by Integrated DNA Technologies (3 mentions) Qiaamp viral rna mini kit, by Qiagen (3 mentions) Chromium single cell 3 library gel bead kit v3, by 10x Genomics (1 mentions) Nextseq 550, by Illumina (1 mentions) Nextera xt dna library preparation kit, by Illumina (1 mentions) Ampure magnetic beads, by Beckman Coulter (1 mentions)

5 protocols using novaseq sp lane

1

SARS-CoV-2 Genomic Sequencing from Saliva

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Viral RNA was extracted from 140 µL of heat-inactivated (30 minutes at 95°C, as part of the protocol detailed in Ranoa et al. [9 (link)]) saliva samples using the QIAamp viral RNA mini kit (QIAGEN); 100 ng of viral RNA was used to generate cDNA using the SuperScript IV first strand synthesis kit (Invitrogen). Viral cDNA was then used to generate sequencing libraries using the Swift SNAP Amplicon SARS CoV2 kit with an additional coverage panel and unique dual indexing (Swift Biosciences), which were sequenced on an Illumina Novaseq SP lane. Data were run through the nf-core/viralrecon workflow (https://nf-co.re/viralrecon/1.1.0) using the Wuhan-Hu-1 reference genome (NCBI accession NC_045512.2). Swift, version 2, primer sequences were trimmed before variant analysis from iVar, version 1.3.1 (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1618-7), retaining all calls with a minimum allele frequency of 0.01 and higher. Viral lineages were called using the Pangolin tool (https://github.com/cov-lineages/pangolin), version 2.4.2, pango, version 1.2.6, and the 5/19/21 version of the pangoLEARN model.
Ke R., Martinez P.P., Smith R.L., Gibson L.L., Achenbach C.J., McFall S., Qi C., Jacob J., Dembele E., Bundy C., Simons L.M., Ozer E.A., Hultquist J.F., Lorenzo-Redondo R., Opdycke A.K., Hawkins C., Murphy R.L., Mirza A., Conte M., Gallagher N., Luo C.H., Jarrett J., Conte A., Zhou R., Farjo M., Rendon G., Fields C.J., Wang L., Fredrickson R., Baughman M.E., Chiu K.K., Choi H., Scardina K.R., Owens A.N., Broach J., Barton B., Lazar P., Robinson M.L., Mostafa H.H., Manabe Y.C., Pekosz A., McManus D.D, & Brooke C.B. (2022). Longitudinal Analysis of SARS-CoV-2 Vaccine Breakthrough Infections Reveals Limited Infectious Virus Shedding and Restricted Tissue Distribution. Open Forum Infectious Diseases, 9(7), ofac192.
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2

SARS-CoV-2 Genomic Sequencing from Saliva

Cited 1 time
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Viral RNA was extracted from 140 uL of heat inactivated (30 minutes at 95°C, as part of protocol detailed in 24 (link)) saliva samples using the QIAamp viral RNA mini kit (QIAGEN). 100ng of viral RNA was used to generate cDNA using the SuperScript IV first strand synthesis kit (Invitrogen). Viral cDNA was then used to generate sequencing libraries using the Swift SNAP Amplicon SARS CoV2 kit with additional coverage panel and unique dual indexing (Swift Biosciences) which were sequenced on an Illumina Novaseq SP lane. Data were run through the nf-core/viralrecon workflow (https://nf-co.re/viralrecon/1.1.0), using the Wuhan-Hu-1 reference genome (NCBI accession NC_045512.2). Swift v2 primer sequences were trimmed prior to variant analysis from iVar version 1.3.1 (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1618-7) retaining all calls with a minimum allele frequency of 0.01 and higher. Viral lineages were called using the Pangolin tool (https://github.com/cov-lineages/pangolin) version 2.4.2, pango version 1.2.6, and the 5/19/21 version of the pangoLEARN model; based on the nomenclature system described in 59 (link).
Ke R., Martinez P.P., Smith R.L., Gibson L.L., Mirza A., Conte M., Gallagher N., Luo C.H., Jarrett J., Zhou R., Conte A., Liu T., Farjo M., Walden K.K., Rendon G., Fields C.J., Wang L., Fredrickson R., Edmonson D.C., Baughman M.E., Chiu K.K., Choi H., Scardina K.R., Bradley S., Gloss S.L., Reinhart C., Yedetore J., Quicksall J., Owens A.N., Broach J., Barton B., Lazar P., Heetderks W.J., Robinson M.L., Mostafa H.H., Manabe Y.C., Pekosz A., McManus D.D, & Brooke C.B. (2022). Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness. Nature microbiology, 7(5), 640-652.
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3

Organoid Single-Cell RNA-Seq Analysis

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Organoids were dissociated. Library preparation was performed with the Chromium Single Cell 3' Library & Gel Bead Kit v.3 (10x Genomics, PN-1000075). Libraries were sequenced on a NextSeq 550 (Illumina) or on a NovaSeq SP lane (Illumina). Quality control and pre-processing was performed using Seurat R package v.3. Visualization and pseudotime analysis were performed using monocle3.
Eichmüller O.L., Corsini N.S., Vértesy Á., Morassut I., Scholl T., Gruber V.E., Peer A.M., Chu J., Novatchkova M., Hainfellner J.A., Paredes M.F., Feucht M, & Knoblich J.A. (2022). Amplification of human interneuron progenitors promotes brain tumors and neurological defects. Science (New York, N.Y.), 375(6579), eabf5546.
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4

SARS-CoV-2 Genomic Sequencing from Saliva

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
Viral RNA was extracted from 140 uL of heat inactivated (30 minutes at 95°C, as part of protocol detailed in 24 (link)) saliva samples using the QIAamp viral RNA mini kit (QIAGEN). 100ng of viral RNA was used to generate cDNA using the SuperScript IV first strand synthesis kit (Invitrogen). Viral cDNA was then used to generate sequencing libraries using the Swift SNAP Amplicon SARS CoV2 kit with additional coverage panel and unique dual indexing (Swift Biosciences) which were sequenced on an Illumina Novaseq SP lane. Data were run through the nf-core/viralrecon workflow (https://nf-co.re/viralrecon/1.1.0), using the Wuhan-Hu-1 reference genome (NCBI accession NC_045512.2). Swift v2 primer sequences were trimmed prior to variant analysis from iVar version 1.3.1 (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1618-7) retaining all calls with a minimum allele frequency of 0.01 and higher. Viral lineages were called using the Pangolin tool (https://github.com/cov-lineages/pangolin) version 2.4.2, pango version 1.2.6, and the 5/19/21 version of the pangoLEARN model; based on the nomenclature system described in 59 (link).
Ke R., Martinez P.P., Smith R.L., Gibson L.L., Mirza A., Conte M., Gallagher N., Luo C.H., Jarrett J., Zhou R., Conte A., Liu T., Farjo M., Walden K.K., Rendon G., Fields C.J., Wang L., Fredrickson R., Edmonson D.C., Baughman M.E., Chiu K.K., Choi H., Scardina K.R., Bradley S., Gloss S.L., Reinhart C., Yedetore J., Quicksall J., Owens A.N., Broach J., Barton B., Lazar P., Heetderks W.J., Robinson M.L., Mostafa H.H., Manabe Y.C., Pekosz A., McManus D.D, & Brooke C.B. (2022). Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness. Nature microbiology, 7(5), 640-652.
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5

FUT2 and FUT3 Amplicon Sequencing

Cited 1 time
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The FUT2 and FUT3 amplicons were purified with AMPure magnetic beads (Beckman Coulter) and pooled in equimolar ratios for each participant. Libraries were prepared with the Nextera XT DNA Library Preparation Kit (Illumina), pooled in equimolar ratios, and sequenced on a NovaSeq SP Lane (300 cycles, 150-bp pair-ended reads; Illumina) at the Australian Genome Research Facility.
The generated paired-end FASTQ files were screened for quality with FastQC version 0.11.9. The human reference genome assembly GRCh38 was indexed with SAMtools version 1.5, and reads were mapped against this reference genome with the Burrows-Wheeler Alignment tool version 0.7.17 [36 (link)] implemented with the mem algorithm. The SAM files were converted to BAM files and sorted with SAMtools version 1.9. The single-nucleotide polymorphisms (SNPs) were then called with the SAMtools mpileup function and the call function implemented in BCFtools version 1.12 [37 (link)]. SNPs were subsequently filtered and annotated with BCFtools.
Donato C.M., Handley A., Byars S.G., Bogdanovic-Sakran N., Lyons E.A., Watts E., Ong D.S., Pavlic D., At Thobari J., Satria C.D., Nirwati H., Soenarto Y, & Bines J.E. (2023). Vaccine Take of RV3-BB Rotavirus Vaccine Observed in Indonesian Infants Regardless of HBGA Status. The Journal of Infectious Diseases, 229(4), 1010-1018.
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