FAIRDOMHub

26 items tagged with 'ISA'.

_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

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Created: 6th Nov 2019 at 14:40, Last updated: 8th Apr 2020 at 16:39

/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

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Created: 6th Nov 2019 at 14:25, Last updated: 8th Apr 2020 at 16:39

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

_p_stRT

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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 11:48, Last updated: 8th Dec 2022 at 17:26

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 15:31, Last updated: 25th Nov 2019 at 23:28

/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

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Created: 6th Nov 2019 at 15:28, Last updated: 25th Nov 2019 at 23:28

/_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

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Created: 6th Nov 2019 at 15:26, Last updated: 25th Nov 2019 at 23:26

/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

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Created: 6th Nov 2019 at 15:25, Last updated: 25th Nov 2019 at 23:28

/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

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Created: 6th Nov 2019 at 15:24, Last updated: 25th Nov 2019 at 23:28

/_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

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Created: 6th Nov 2019 at 15:22, Last updated: 25th Nov 2019 at 23:26

/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

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Created: 6th Nov 2019 at 15:19, Last updated: 25th Nov 2019 at 23:28

/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

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Created: 6th Nov 2019 at 14:38, Last updated: 25th Nov 2019 at 23:28

/_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

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Created: 6th Nov 2019 at 14:35, Last updated: 25th Nov 2019 at 23:26

/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

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Created: 6th Nov 2019 at 14:31, Last updated: 25th Nov 2019 at 23:28

/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

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Created: 6th Nov 2019 at 14:22, Last updated: 25th Nov 2019 at 23:28

/_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

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Created: 6th Nov 2019 at 14:21, Last updated: 25th Nov 2019 at 23:26

/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

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Created: 6th Nov 2019 at 14:18, Last updated: 25th Nov 2019 at 23:28

/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

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Created: 6th Nov 2019 at 14:15, Last updated: 25th Nov 2019 at 23:28

/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

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Created: 6th Nov 2019 at 14:13, Last updated: 25th Nov 2019 at 23:28

/presentations/README.MD

_p_stRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 6th Nov 2019 at 14:12, Last updated: 25th Nov 2019 at 23:28

/_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

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Created: 6th Nov 2019 at 14:10, Last updated: 25th Nov 2019 at 23:28

/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

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Created: 6th Nov 2019 at 14:07, Last updated: 25th Nov 2019 at 23:28

/README.MD

_p_stRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 6th Nov 2019 at 14:01, Last updated: 25th Nov 2019 at 16:16

/Metadata_files.md

_p_stRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 6th Nov 2019 at 14:02, Last updated: 25th Nov 2019 at 23:28

/reports/README.MD

_p_stRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 6th Nov 2019 at 14:04, Last updated: 25th Nov 2019 at 23:28

/_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

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Created: 6th Nov 2019 at 13:58, Last updated: 25th Nov 2019 at 16:10

/_p_stRT_TREE.TXT

_p_stRT

Creators: Maja Zagorscak, Andrej Blejec

Submitter: Maja Zagorscak

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 6th Nov 2019 at 13:51, Last updated: 25th Nov 2019 at 23:27