/presentations/Figure2.pdf

_p_stRT/_I_STRT pipeline

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3157.1

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/reports/SupplementaryTableS2

Supplementary Table S2 - Detailed de novo assemblies information table. Primary potato transcriptome assemblies summary listing parameters used for short-read de novo assembly generation. Layer _p_stRT/_I_STRT/_S_02_denovo/reports/

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3091.1

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/reports/SupplementaryTableS1

Supplementary Table S1 - Detailed sample information table used to generate the de novo transcriptome assemblies. Raw and processed reads summary. Layer _p_stRT/_I_STRT/ _S_01_sequences/reports

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3090.1

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pISA-tree - a data management framework for life science research projects using a standardised directory tree

Abstract (Expand)

Abstract We have developed pISA-tree, a straightforward and flexible data management solution for organisation of life science project-associated research data and metadata. It enables on the fly …and metadata. It enables on the fly creation of enriched directory tree structure ( p roject/ I nvestigation/ S tudy/ A ssay), via a series of sequential batch files in a standardised manner based upon the ISA metadata framework. Metadata, according to the system-provided metadata templates, is generated in parallel at each level. The system supports reproducible research and is in accordance with the Open Science initiative and FAIR principles. Compared with similar frameworks, it does not require any systems administration and maintenance as it can be run on a personal computer or network drive. It is complemented with two R packages, pisar and seekr , where the former facilitates integration of the pISA-tree datasets into bioinformatic pipelines and the latter enables synchronisation with the FAIRDOMHub public repository using the SEEK API. Source code and detailed documentation of pISA-tree and its supporting R packages are available from https://github.com/NIB-SI/pISA-tree . We demonstrate the usability of pISA-tree with two examples of medium sized life science projects. Accordingly, it is suitable and also currently used to manage larger projects including several partners from different countries. Since pISA-tree was initiated by end user requirements with an emphasis on practicality, it will facilitate adoption of FAIR data management practices and open science principles.

Authors: Marko Petek, Maja Zagorščak, Andrej Blejec, Živa Ramšak, Anna Coll, Špela Baebler, Kristina Gruden

Date Published: 21st Nov 2021

Publication Type: Journal

Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

Abstract (Expand)

Background: Although the reference genome of Solanum tuberosum group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid group … Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research and its subsequent applications in breeding. Results: For the DM genome assembly, two only partially-overlapping gene models exist differing in a unique set of genes and intron/exon structure predictions. First step was to merge and manually curate the merged gene model, creating a union of genes in Phureja scaffold. We next compiled available RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using CLC, Trinity, Velvet, and rnaSPAdes de novo assemblers using different settings to test for optimal outcome. In addition, for cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. Revised EvidentialGene redundancy-reducing pipeline was employed to produce accurate and complete cultivar-specific transcriptomes from assemblers output, as well as to attain the pan-transcriptome. Due to being the most diverse dataset in terms of tissues (stem, seedlings and roots) and experimental conditions, cv. Désirée was the most complete transcriptome (95.8% BUSCO completeness). For cv. Rywal and breeding clone PW363 data were available for leaf samples only and the resulting transcriptomes were less complete than cv. Désirée (89.8% and 89.3% BUSCO completeness, respectively). Cross comparison of these cultivar-specific transcriptomes and merged DM gene model suggests that the core potato transcriptome is comprised of 16,339 genes. The pan-transcriptome contains a total of 95,779 transcripts, of which 54,614 transcripts are not present in the Phureja genome. These represent the variants of the novel genes found in the potato pan-genome. Conclusions: Our analysis shows that the available gene model of double-monoploid potato from group Phureja is, to some degree, not complete. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput -omics analyses, and future breeding programmes.

Authors: Marko Petek, Maja Zagorščak, Živa Ramšak, Sheri Sanders, Elizabeth Tseng, Mohamed Zouine, Anna Coll, Kristina Gruden

Date Published: No date defined

Publication Type: Not specified

Nutzung von Persistent Identifiern zur Umsetzung der FAIR-Prinzipien in Datenablageplattformen für die medizinische Forschung

Abstract

Not specified

Editor:

Date Published: 24th Oct 2017

Publication Type: Not specified

FAIR Data, Operations and Model management for Systems Biology and Systems Medicine Projects

FAIR Data, Operations and Model management for Systems Biology and Systems Medicine Projects given at 1st Conference of the European Association of Systems Medicine, 26-28 October 2016, Berlin. the FAIRDOM project is described.

Creator: Carole Goble

Submitter: Carole Goble

External Link
Wolfgang Müller: Introduction to Data Management
No description specified

Creator: Wolfgang Müller

Submitter: Carsten Fortmann-Grote

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pISA/README.MD at projects · NIB-SI/pISA · GitHub

pISA-tree: Standard project directory tree (ISA-tab compliant) - NIB-SI/pISA https://github.com/NIB-SI/pISA/

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

/reports/README.MD

_p_stRT/_I_STRT/_S_04_stPanTr

Creators: Maja Zagorscak, Ziva Ramsak

Submitter: Maja Zagorscak

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/_STUDY_METADATA.TXT

_p_stRT/_I_STRT/_S_04_stPanTr

Creators: Maja Zagorscak, Ziva Ramsak

Submitter: Maja Zagorscak

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/README.MD

_p_stRT/_I_STRT/_S_04_stPanTr

Creators: Maja Zagorscak, Ziva Ramsak

Submitter: Maja Zagorscak

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/reports/README.MD

_p_stRT/_I_STRT/_S_03_stCuSTr

Creators: Maja Zagorscak, Ziva Ramsak

Submitter: Maja Zagorscak

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/_STUDY_METADATA.TXT

_p_stRT/_I_STRT/_S_03_stCuSTr

Creators: Maja Zagorscak, Ziva Ramsak

Submitter: Maja Zagorscak

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/README.MD

_p_stRT/_I_STRT/_S_03_stCuSTr

Creators: Maja Zagorscak, Ziva Ramsak

Submitter: Maja Zagorscak

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/reports/README.MD

_p_stRT/_I_STRT/_S_02_denovo

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

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/_STUDY_METADATA.TXT

_p_stRT/_I_STRT/_S_02_denovo

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

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/README.MD

_p_stRT/_I_STRT/_S_02_denovo

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

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/reports/README.MD

_p_stRT/_I_STRT/_S_01_sequences

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

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/_STUDY_METADATA.TXT

_p_stRT/_I_STRT/_S_01_sequences

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

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/README.MD

_p_stRT/_I_STRT/_S_01_sequences

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

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/presentations/README.MD

_p_stRT/_I_STRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

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/reports/README.MD

_p_stRT/_I_STRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

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/presentations/README.MD

_p_stRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

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/_INVESTIGATION_METADATA.TXT

_p_stRT/_I_STRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

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/README.MD

_p_stRT/_I_STRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

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/README.MD

_p_stRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

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/Metadata_files.md

_p_stRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

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/reports/README.MD

_p_stRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

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/_PROJECT_METADATA.TXT

_p_stRT

Creators: Maja Zagorscak, Kristina Gruden, Marko Petek, Ziva Ramsak, Anna Coll Rius

Submitter: Maja Zagorscak

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/_p_stRT_TREE.TXT

_p_stRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

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