FAIRDOMHub

31 items tagged with 'FAIR'.

/presentations/Figure2.pdf

_p_stRT

_p_stRT/_I_STRT pipeline

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3157.1

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 16th Nov 2019 at 11:49, Last updated: 25th Nov 2019 at 00:33

/reports/SupplementaryTableS2

_p_stRT

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

Investigations: _I_STRT

Studies: SupplementaryInformation

Assays: Supplementary Information

Download

Created: 6th Nov 2019 at 15:40, Last updated: 8th Apr 2020 at 18:39

/reports/SupplementaryTableS1

_p_stRT

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

Investigations: _I_STRT

Studies: SupplementaryInformation

Assays: Supplementary Information

Download

Created: 6th Nov 2019 at 15:25, Last updated: 8th Apr 2020 at 18:39

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

pISA-tree

(Show All)

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 …

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

Date Published: 21st Nov 2021

Publication Type: Journal

DOI: 10.1101/2021.11.18.468977

Citation: biorxiv;2021.11.18.468977v2,[Preprint]

Created: 5th Sep 2022 at 13:53, Last updated: 8th Dec 2022 at 18:26

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

_p_stRT

(Show All)

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

DOI: 10.1101/845818

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

Created: 19th Nov 2019 at 12:48, Last updated: 8th Dec 2022 at 18:26

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

WG Infrastructure for Translational Research

Abstract

Not specified

Editor:

Date Published: 24th Oct 2017

Publication Type: Not specified

Citation: Knopp C. Nutzung von Persistent Identifiern zur Umsetzung der FAIR-Prinzipien in Datenablageplattformen für die medizinische Forschung [Bachelorarbeit]. Göttingen: Georg-August-Universität; 2017.

Created: 17th Oct 2017 at 20:58, Last updated: 8th Dec 2022 at 18:26

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

FAIRDOM

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

Created: 19th Oct 2021 at 17:06, Last updated: 19th Oct 2021 at 17:06

Wolfgang Müller: Introduction to Data Management

MPIEvolBio-SciComp

No description specified

Creator: Wolfgang Müller

Submitter: Carsten Fortmann-Grote

Download

Created: 18th May 2021 at 20:51, Last updated: 18th May 2021 at 21:24

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

pISA-tree, _p_stRT

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

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 6th Nov 2019 at 16:31, Last updated: 25th Nov 2019 at 00:28

/reports/README.MD

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr

Creators: Maja Zagorscak, Ziva Ramsak

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 16:28, Last updated: 25th Nov 2019 at 00:28

/_STUDY_METADATA.TXT

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr

Creators: Maja Zagorscak, Ziva Ramsak

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 16:26, Last updated: 25th Nov 2019 at 00:26

/README.MD

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr

Creators: Maja Zagorscak, Ziva Ramsak

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 16:25, Last updated: 25th Nov 2019 at 00:28

/reports/README.MD

_p_stRT

_p_stRT/_I_STRT/_S_03_stCuSTr

Creators: Maja Zagorscak, Ziva Ramsak

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 16:24, Last updated: 25th Nov 2019 at 00:28

/_STUDY_METADATA.TXT

_p_stRT

_p_stRT/_I_STRT/_S_03_stCuSTr

Creators: Maja Zagorscak, Ziva Ramsak

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 16:22, Last updated: 25th Nov 2019 at 00:26

/README.MD

_p_stRT

_p_stRT/_I_STRT/_S_03_stCuSTr

Creators: Maja Zagorscak, Ziva Ramsak

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 16:19, Last updated: 25th Nov 2019 at 00:28

/reports/README.MD

_p_stRT

_p_stRT/_I_STRT/_S_02_denovo

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 15:38, Last updated: 25th Nov 2019 at 00:28

/_STUDY_METADATA.TXT

_p_stRT

_p_stRT/_I_STRT/_S_02_denovo

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 15:35, Last updated: 25th Nov 2019 at 00:26

/README.MD

_p_stRT

_p_stRT/_I_STRT/_S_02_denovo

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 15:31, Last updated: 25th Nov 2019 at 00:28

/reports/README.MD

_p_stRT

_p_stRT/_I_STRT/_S_01_sequences

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 15:22, Last updated: 25th Nov 2019 at 00:28

/_STUDY_METADATA.TXT

_p_stRT

_p_stRT/_I_STRT/_S_01_sequences

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 15:21, Last updated: 25th Nov 2019 at 00:26

/README.MD

_p_stRT

_p_stRT/_I_STRT/_S_01_sequences

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 15:18, Last updated: 25th Nov 2019 at 00:28

/presentations/README.MD

_p_stRT

_p_stRT/_I_STRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 15:15, Last updated: 25th Nov 2019 at 00:28

/reports/README.MD

_p_stRT

_p_stRT/_I_STRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 15:13, Last updated: 25th Nov 2019 at 00:28

/presentations/README.MD

_p_stRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 15:12, Last updated: 25th Nov 2019 at 00:28

/_INVESTIGATION_METADATA.TXT

_p_stRT

_p_stRT/_I_STRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 15:10, Last updated: 25th Nov 2019 at 00:28

/README.MD

_p_stRT

_p_stRT/_I_STRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 15:07, Last updated: 25th Nov 2019 at 00:28

/README.MD

_p_stRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 15:01, Last updated: 25th Nov 2019 at 17:16

/Metadata_files.md

_p_stRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 15:02, Last updated: 25th Nov 2019 at 00:28

/reports/README.MD

_p_stRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 15:04, Last updated: 25th Nov 2019 at 00:28

/_PROJECT_METADATA.TXT

_p_stRT

(Show All)

_p_stRT

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

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 14:58, Last updated: 25th Nov 2019 at 17:10

/_p_stRT_TREE.TXT

_p_stRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 6th Nov 2019 at 14:51, Last updated: 25th Nov 2019 at 00:27