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Part 1: Document Description
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Citation |
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Title: |
Educational dataset: Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections |
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Identification Number: |
doi:10.18710/FFANM0 |
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Distributor: |
DataverseNO |
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Date of Distribution: |
2023-10-30 |
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Version: |
1 |
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Bibliographic Citation: |
Michoel, Tom, 2023, "Educational dataset: Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections", https://doi.org/10.18710/FFANM0, DataverseNO, V1 |
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Citation |
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Title: |
Educational dataset: Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections |
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Identification Number: |
doi:10.18710/FFANM0 |
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Authoring Entity: |
Michoel, Tom (University of Bergen) |
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Other identifications and acknowledgements: |
Morrison, Liam (The University of Edinburgh) |
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Other identifications and acknowledgements: |
Jayaraman, Siddharth (The University of Edinburgh) |
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Producer: |
Morrison, Liam |
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Date of Production: |
2018-11-01 |
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Grant Number: |
UF090083 |
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Grant Number: |
UF140610 |
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Grant Number: |
RG110378 |
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Grant Number: |
BB/J004227/1 |
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Grant Number: |
BB/J004235/1 |
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Grant Number: |
BBS/E/D/20002173 |
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Distributor: |
DataverseNO |
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Distributor: |
University of Bergen |
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Access Authority: |
Michoel, Tom |
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Depositor: |
Michoel, Tom |
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Date of Deposit: |
2023-09-22 |
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Holdings Information: |
https://doi.org/10.18710/FFANM0 |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences, Bioinformatics, Bioinformatics, Transcriptomics, assay by long read sequencer, Trypanosoma brucei TREU927 |
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Abstract: |
<p> The dataset is created for use in the teaching of the undergraduate course <a href="https://www.uib.no/en/course/BINF200">BINF200 - Analysis of Biological Sequences and Structures</a>, first used in Autumn 2023. </p> <p> The dataset contains (1) the processed, filtered and sample annotated sequenced reads in fasta format from Jayaraman et al (2019), repackaged in individual sample files and (2) a local database of variant surface glycoprotein (VSG) sequences in the Trypanosoma brucei reference strain TREU927. </p> <p> The original data are available in GEO dataset <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3151449">GSE114843</a>. Further details about the original data are available at <a href="https://github.com/siddharthjayaraman/longread-application">github.com/siddharthjayaraman/longread-application</a> (archived at <a href="https://doi.org/10.5281/zenodo.10043245">https://doi.org/10.5281/zenodo.10043245</a>). <p> <p> The database of TREU927 VSG sequences is based on the (outdated) TREU927 genome v26. It is included for educational purposes and to reproduce results from the original publication. For research purposes always use the most recent genome version at <a href="https://tritrypdb.org/">tritrypdb.org</a>. </p> <p> The code that was used to generate the present data as well as educational notebooks of downstream analyses are available at <a href="https://github.com/tmichoel/BINF200-bio-sequences-structures">github.com/tmichoel/BINF200-bio-sequences-structures</a> (archived at <a href="https://doi.org/10.5281/zenodo.10043222">https://doi.org/10.5281/zenodo.10043222</a>). <p> Consider using Tree View to browse the files efficiently. |
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Kind of Data: |
sequencing data |
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Kind of Data: |
machine-readable text |
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Kind of Data: |
blast database |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Notes: |
<a href="http://creativecommons.org/publicdomain/zero/1.0">CC0 1.0</a> |
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Other Study Description Materials |
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Related Studies |
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<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114843">GSE114843</a> |
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<a href="https://github.com/siddharthjayaraman/longread-application">github.com/siddharthjayaraman/longread-application</a> archived at <a href="https://doi.org/10.5281/zenodo.10043245">https://doi.org/10.5281/zenodo.10043245</a> |
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<a href="https://github.com/tmichoel/BINF200-bio-sequences-structures">github.com/tmichoel/BINF200-bio-sequences-structures</a> archived at <a href="https://doi.org/10.5281/zenodo.10043222">https://doi.org/10.5281/zenodo.10043222</a> |
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Related Publications |
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Citation |
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Title: |
Jayaraman S, Harris C, Paxton E, Donachie A-M, Vaikkinen H, McCulloch R, et al. (2019) Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. PLoS Negl Trop Dis 13(4): e0007262. |
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Identification Number: |
10.1371/journal.pntd.0007262 |
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Bibliographic Citation: |
Jayaraman S, Harris C, Paxton E, Donachie A-M, Vaikkinen H, McCulloch R, et al. (2019) Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. PLoS Negl Trop Dis 13(4): e0007262. |
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Label: |
00_README.txt |
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Text: |
README file |
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Notes: |
text/plain |
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Label: |
PacBio_VSG_filtered_reads_balbc_10_0.fasta |
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Notes: |
application/octet-stream |
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Label: |
PacBio_VSG_filtered_reads_balbc_10_1.fasta |
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Notes: |
application/octet-stream |
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Label: |
PacBio_VSG_filtered_reads_balbc_10_2.fasta |
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Notes: |
application/octet-stream |
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Label: |
PacBio_VSG_filtered_reads_balbc_10_4.fasta |
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Notes: |
application/octet-stream |
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Label: |
PacBio_VSG_filtered_reads_balbc_10_5.fasta |
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Notes: |
application/octet-stream |
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Label: |
PacBio_VSG_filtered_reads_balbc_12_1.fasta |
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Notes: |
application/octet-stream |
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Label: |
PacBio_VSG_filtered_reads_balbc_12_2.fasta |
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Notes: |
application/octet-stream |
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Label: |
PacBio_VSG_filtered_reads_balbc_12_3.fasta |
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Notes: |
application/octet-stream |
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PacBio_VSG_filtered_reads_balbc_12_4.fasta |
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Notes: |
application/octet-stream |
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Label: |
PacBio_VSG_filtered_reads_balbc_12_5.fasta |
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Notes: |
application/octet-stream |
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PacBio_VSG_filtered_reads_balbc_3_0.fasta |
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Notes: |
application/octet-stream |
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Label: |
PacBio_VSG_filtered_reads_balbc_3_1.fasta |
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Notes: |
application/octet-stream |
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Label: |
PacBio_VSG_filtered_reads_balbc_3_2.fasta |
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Notes: |
application/octet-stream |
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PacBio_VSG_filtered_reads_balbc_3_3.fasta |
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application/octet-stream |
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PacBio_VSG_filtered_reads_balbc_3_4.fasta |
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Notes: |
application/octet-stream |
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PacBio_VSG_filtered_reads_balbc_6_0.fasta |
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Notes: |
application/octet-stream |
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Label: |
PacBio_VSG_filtered_reads_balbc_6_1.fasta |
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Notes: |
application/octet-stream |
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Label: |
PacBio_VSG_filtered_reads_balbc_6_2.fasta |
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Notes: |
application/octet-stream |
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PacBio_VSG_filtered_reads_balbc_6_4.fasta |
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Notes: |
application/octet-stream |
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Label: |
PacBio_VSG_filtered_reads_balbc_6_5.fasta |
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Notes: |
application/octet-stream |
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Label: |
PacBio_VSG_filtered_reads.fasta |
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Text: |
Original fasta file with filtered sequence reads from all samples. |
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Notes: |
application/octet-stream |
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TREU927-v26_VSGTranscripts.fasta |
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Notes: |
application/octet-stream |
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Label: |
TREU927-v26_VSGTranscripts.fasta.nhr |
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Notes: |
application/octet-stream |
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Label: |
TREU927-v26_VSGTranscripts.fasta.nin |
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Notes: |
application/octet-stream |
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TREU927-v26_VSGTranscripts.fasta.nsq |
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Notes: |
application/octet-stream |