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Part 1: Document Description
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Citation |
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Title: |
Replication Data for: Enrichment approach for unbiased sequencing of respiratory syncytial virus directly from clinical samples |
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Identification Number: |
doi:10.7910/DVN/28LOAI |
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Distributor: |
Harvard Dataverse |
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Date of Distribution: |
2021-03-17 |
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Version: |
3 |
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Bibliographic Citation: |
Waweru, Jacqueline W.; de Laurent, Zaydah; Kamau, Everlyn; Said, Khadija; Gicheru, Elijah; Mutunga, Martin; Kibet, Caleb; Kinyua, Johnson; Nokes, David James; Sande, Charles; Githinji, George, 2021, "Replication Data for: Enrichment approach for unbiased sequencing of respiratory syncytial virus directly from clinical samples", https://doi.org/10.7910/DVN/28LOAI, Harvard Dataverse, V3 |
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Citation |
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Title: |
Replication Data for: Enrichment approach for unbiased sequencing of respiratory syncytial virus directly from clinical samples |
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Identification Number: |
doi:10.7910/DVN/28LOAI |
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Authoring Entity: |
Waweru, Jacqueline W. (Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya; KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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de Laurent, Zaydah (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Kamau, Everlyn (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Said, Khadija (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Gicheru, Elijah (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Mutunga, Martin (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Kibet, Caleb (Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya) |
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Kinyua, Johnson (Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya) |
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Nokes, David James (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Sande, Charles (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Githinji, George (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Biochemistry and Biotechnology, Pwani University) |
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Distributor: |
Harvard Dataverse |
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Access Authority: |
Waweru, Jacqueline W. |
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Access Authority: |
Nokes, David James |
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Access Authority: |
Githinji, George |
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Access Authority: |
The data governance office |
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Depositor: |
Waweru, Jacqueline W. |
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Date of Deposit: |
2021-03-15 |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences, metagenomics, sequencing, SISPA, RSV, centrifugal processing, Endoh primers, DNase, RNA |
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Abstract: |
<p>This is a replication dataset for the manuscript titled: "<a href="">Enrichment approach for unbiased sequencing of respiratory syncytial virus directly from clinical samples</a>."</p> <p>The data contains the results obtained after optimizing a metagenomics sequencing protocol for respiratory viruses with the main virus of interest being the respiratory syncytial virus (RSV); a leading cause of lower respiratory tract infections among children under the age of five. The Oxford Nanopore Technology MinION device was used for sequencig in this study. Besides, all the viral load results, nucleic acid concentrations obtained after performing real time PCR have also been included here.</p> |
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Notes: |
<strong>Instruction for running analysis code</strong> <p>Data analysis R codes are numbered 1 to 3. The order ofR scripts is as follows: <br> <ol> <li> 1_boxplots_analysis: Contains codes used in generating all the box-plots generated from this data. </li> <li> 2_taxonomic_analysis:Contains codes that were used in analyzing the Kraken2 taxonomic classification reports. </li> <li> 3_MinION.sh: bash script containing the codes used in running Vsearch and primer matching using seqkit. </li> </ol> The R codes and datasets were generated using R version 3.6. In addition, Primers.fasta - A fasta file containing all the Endoh primers used in this study RSV_centroid.fasta - A fasta file containing the centroid sequence generated from the Illumina consensus sequences using Vsearch. </p> |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Citation Requirement: |
<p>Publications based on this data collection should acknowledge this source by means of bibliographic citation.</p> |
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Notes: |
<p>This data is licensed under the <a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a> <a href="https://creativecommons.org/licenses/by/4.0/legalcode"><img src="https://i.creativecommons.org/l/by/3.0/88x31.png"> </a> </p> |
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Other Study Description Materials |
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Label: |
1_boxplots_script.R |
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Text: |
Contains codes used in generating all the box-plots generated from this data |
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Notes: |
type/x-r-syntax |
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Label: |
2_taxonomic_analysis.R |
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Text: |
Contains codes that were used in analyzing the Kraken2 taxonomic classification reports |
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Notes: |
type/x-r-syntax |
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Label: |
3_MinION pipeline.sh |
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Text: |
bash script containing the codes used in running Vsearch and primer matching using seqkit |
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Notes: |
text/x-sh |
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Label: |
bacterial_contamination_gel.jpg |
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Notes: |
image/jpeg |
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bacterial_contamination_reduction_gel.jpg |
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Notes: |
image/jpeg |
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data.zip |
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Text: |
Contains all data files used in the analysis |
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Notes: |
application/zip |
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JWaweru_Data_Codebook.pdf |
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Notes: |
application/pdf |
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JWaweru_Data_Readme.txt |
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Notes: |
text/plain |
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primers.fasta |
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Text: |
A fasta file containing all the Endoh primers used in this study |
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Notes: |
application/octet-stream |
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Label: |
RSV_centroid.fasta |
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Text: |
A fasta file containing the centroid sequence generated from the Illumina consensus sequences using Vsearch |
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Notes: |
application/octet-stream |
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Label: |
sispa_gel.jpg |
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Notes: |
image/jpeg |