Details about this organism
Synonyms (1)Solanum tuberosum subsp. tuberosum
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Strain details
Name | Provider name | Provider's strain ID | Genotypes | Phenotypes | Synonym | Comments | Based on |
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Related items
National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
project: _p_stRT Short Name: stRT Title: Solanum tuberosum Reference Transcriptomes Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato pISA projects path: ../pISA-Projects Local pISA-tree organisation: National Institute of Biology pISA project creation date: 2019-10-22 pISA project creator: Maja Zagorscak, Ziva Ramsak, Marko Petek Project funding code: This project was supported by the Slovenian Research Agency (grants P4-0165, J4-4165, J4-7636, ...
Programme: NIBSys
Public web page: http://www.nib.si/eng/index.php/systems-biology
Start date: 1st Dec 2017
End date: 1st Jan 2020
Organisms: Solanum tuberosum, Potato virus Y
In this project, the involved partners are trying to develop the knowledge base that will enable the breeding of new potato varieties, tolerant to multiple environmental stressors.
Programme: NIBSys
Public web page: https://adapt.univie.ac.at/
Start date: 1st Jul 2020
End date: 30th Jun 2024
Organisms: Solanum tuberosum
Time series response of potato cv. Désirée, which is tolerant to PVY infection, was analysed in both inoculated as well as upper non-inoculated leaves. Additionally, transgenic plants deficient in accumulation of salicylic acid (NahG- Désirée) were studied in the same setting.
This investigation is published under the CC BY 4.0 license.
Programme: NIBSys
Public web page: Not specified
Organisms: Potato virus Y, Solanum tuberosum
Description of observed phenotypic variables in the MOA investigation.
Submitter: Ziva Ramsak
Assay type: Phenotype observation
Technology type: Imaging
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Organisms: Solanum tuberosum, Potato virus Y
SOPs: No SOPs
Data files: MOA2010-05_1A_disease-symptoms, MOA2010-05_1A_disease-symptoms-images, MOA_Multiomics-Analysis_Phenodata-n-MIAPPE
Snapshots: Snapshot 1
Submitter: Ziva Ramsak
Assay type: Phenotype observation
Technology type: Leaf Chamber Fluorometer
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Organisms: Solanum tuberosum, Potato virus Y
SOPs: No SOPs
Data files: MOA2010-05_1B_photosynthetic-activity, MOA2010-05_1B_photosynthetic-activity_LM, MOA_Multiomics-Analysis_Phenodata-n-MIAPPE
Snapshots: No snapshots
Submitter: Ziva Ramsak
Assay type: Q_PCR
Technology type: qPCR
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Organisms: Solanum tuberosum, Potato virus Y
SOPs: No SOPs
Data files: MOA2010-05_1C_pathogen-abundance_qPCR, MOA_Multiomics-Analysis_Phenodata-n-MIAPPE
Snapshots: No snapshots
Submitter: Ziva Ramsak
Assay type: Gene Expression Profiling
Technology type: Custom Array
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Organisms: Solanum tuberosum, Potato virus Y
SOPs: No SOPs
Data files: MOA2010-05_2_transcriptomics_microarrays_GEO, MOA2010-05_2_transcriptomics_microarrays_R-code, MOA2010-05_2_transcriptomics_microarrays_R-code..., MOA2010-05_2_transcriptomics_microarrays_logFC, MOA2010-05_2_transcriptomics_microarrays_normal..., MOA_Multiomics-Analysis_Phenodata-n-MIAPPE
Snapshots: No snapshots
Submitter: Ziva Ramsak
Assay type: Q_PCR
Technology type: qPCR
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Organisms: Solanum tuberosum, Potato virus Y
SOPs: No SOPs
Data files: MOA2010-05_2_transcriptomics_qPCR, MOA2010-05_2_transcriptomics_qPCR_MIQE, MOA_Multiomics-Analysis_Phenodata-n-MIAPPE
Snapshots: No snapshots
Submitter: Ziva Ramsak
Assay type: MicroRNA Profiling
Technology type: Next generation sequencing
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Organisms: Solanum tuberosum, Potato virus Y
SOPs: No SOPs
Data files: MOA2010-05_3_sRNAomics_sRNA-Seq_GEO, MOA2010-05_3_sRNAomics_sRNA-Seq_R-code, MOA2010-05_3_sRNAomics_sRNA-Seq_miRNAs_counts, MOA2010-05_3_sRNAomics_sRNA-Seq_miRNAs_counts_RPM, MOA2010-05_3_sRNAomics_sRNA-Seq_miRNAs_logFC, MOA2010-05_3_sRNAomics_sRNA-Seq_phasiRNAs_counts, MOA2010-05_3_sRNAomics_sRNA-Seq_phasiRNAs_count..., MOA2010-05_3_sRNAomics_sRNA-Seq_phasiRNAs_logFC, MOA2010-05_3_sRNAomics_sRNA-Seq_vsiRNAs_counts, MOA2010-05_3_sRNAomics_sRNA-Seq_vsiRNAs_counts_RPM, MOA_Multiomics-Analysis_Phenodata-n-MIAPPE
Snapshots: No snapshots
Submitter: Ziva Ramsak
Assay type: Q_PCR
Technology type: qPCR
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Organisms: Solanum tuberosum, Potato virus Y
SOPs: No SOPs
Data files: MOA2010-05_3_sRNAomics_qPCR, MOA2010-05_3_sRNAomics_qPCR_MIQE, MOA_Multiomics-Analysis_Phenodata-n-MIAPPE
Snapshots: No snapshots
Submitter: Ziva Ramsak
Assay type: Bioinformatics
Technology type: Interactions
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Organisms: Solanum tuberosum, Potato virus Y
SOPs: No SOPs
Data files: MOA2010-05_3C_sRNAomics_bioinformatics_PHAS-loci, MOA2010-05_3C_sRNAomics_bioinformatics_miRNA-novel, MOA2010-05_3C_sRNAomics_bioinformatics_sRNA-tar..., MOA2010-05_3C_sRNAomics_bioinformatics_sRNA-tar..., MOA2010-05_3C_sRNAomics_bioinformatics_sRNA-tar..., MOA_Multiomics-Analysis_Phenodata-n-MIAPPE
Snapshots: No snapshots
Submitter: Ziva Ramsak
Assay type: Degradome-Seq
Technology type: Next generation sequencing
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Organisms: Solanum tuberosum, Potato virus Y
SOPs: No SOPs
Data files: MOA2010-05_4_degradomics_Degradome-Seq_GEO, MOA2010-05_4_degradomics_Degradome-Seq_targets-..., MOA2010-05_4_degradomics_Degradome-Seq_targets-..., MOA_Multiomics-Analysis_Phenodata-n-MIAPPE
Snapshots: No snapshots
Submitter: Ziva Ramsak
Assay type: Metabolite Profiling
Technology type: Gas Chromatography Mass Spectrometry
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2013-12
Organisms: Solanum tuberosum, Potato virus Y
SOPs: No SOPs
Data files: MOA2013-12_1_hormonomics_GCMS, MOA2013-12_1_hormonomics_GCMS_ANOVA-groups, MOA2013-12_1_hormonomics_R-code, MOA_Multiomics-Analysis_Phenodata-n-MIAPPE
Snapshots: No snapshots
Submitter: Ziva Ramsak
Assay type: Protein Quantification
Technology type: Orbitrap Velos
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Organisms: Solanum tuberosum, Potato virus Y
SOPs: No SOPs
Data files: MOA2010-05_5_proteomics_Orbitrap-MaxQuant, MOA2010-05_5_proteomics_Orbitrap-MaxQuant_logFC, MOA2010-05_5_proteomics_Orbitrap-MaxQuant_peptides, MOA2010-05_5_proteomics_Orbitrap-SpectralCounts, MOA2010-05_5_proteomics_Orbitrap-SpectralCounts..., MOA2010-05_5_proteomics_Orbitrap-SpectralCounts..., MOA_Multiomics-Analysis_Phenodata-n-MIAPPE
Snapshots: No snapshots
Assay: _A_01_evigene Short Name: 01_evigene Assay Class: DRY Assay Type: evigene Title: EvidentialGene tr2aacds.pl VERSION 2016.07.11 Description: See http://eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Integration
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum, Potato virus Y
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /intermediate_tr2aacds_Desiree.tar.gz, /intermediate_tr2aacds_PW363.tar.gz.aa, /intermediate_tr2aacds_PW363.tar.gz.ab, /intermediate_tr2aacds_Rywal.tar.gz, /output/output.tar, /scripts/01_run_commands.sh, /scripts/my_tr2aacds.sh, /scripts/run_tr2aacds.sh
Snapshots: Snapshot 1
Assay: _A_02.1_BUSCO Short Name: 02.1_BUSCO Assay Class: DRY Assay Type: BUSCO Title: BUSCO on assemblies and tr2aacds output Description: BUSCO on assemblies and tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Validation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar
Snapshots: Snapshot 1
Assay: _A_02.2_assembly-contribution-count Short Name: 02.2_assembly-contribution-count Assay Class: DRY Assay Type: count Title: assembly contribution count Description: assembly contribution count, input/output tr2aacds pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/input.tar, /intermediate_Desiree.tar.gz, /intermediate_PW363.tar.gz, /intermediate_Rywal.tar.gz, /output/output.tar, /reports/SupplementaryFigure1.pdf, /reports/SupplementaryFigure2.pdf, /reports/SupplementaryFigure3.pdf, /reports/SupplementaryTableS6, /scripts/scripts.tar
Snapshots: Snapshot 1
Assay: _A_02.3_InterProScan Short Name: 02.3_InterProScan Assay Class: DRY Assay Type: InterProScan Title: InterProScan on tr2aacds output Description: InterProScan on tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Annotation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /intermediate/intermediate.tar, /output/Desiree_IPS_filtered_aggregated_filtere..., /output/PW363_IPS_filtered_aggregated_filtered.tsv, /output/Rywal_IPS_filtered_aggregated_filtered.tsv, /reports/IPS_PowerQuery_PivotTable.xlsx, /scripts/01_potato_tr_evigene_IPS_commands.txt, /scripts/02_reshape_merge_aggregate_filter.Rmd
Snapshots: Snapshot 1
Assay: _A_02.4_STAR Short Name: 02.4_STAR Assay Class: DRY Assay Type: STAR Title: mapping reads back to evigene .tr output Description: mapping reads back to evigene .tr output using STAR to check the percentage of reads that map pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Validation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /output/output_STAR_logs-n-SJ.tar.gz, /output/samtoolsCoverage.zip, /reports/summaryCounts&SJ.xlsx, /scripts/STAR_commands.txt
Snapshots: Snapshot 1
Assay: _A_02.5_STARlong_matchAnnot Short Name: 02.5_STARlong_matchAnnot Assay Class: DRY Assay Type: matchAnnot Title: potato transcriptome v2 (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations Description: potato initial transcriptome (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None ...
Submitter: Maja Zagorscak
Biological problem addressed: Annotation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /output/output_1_STARlong-logs-n-SJ.tar.gz, /output/output_2_matchAnnot-parsed-txt.tar.gz, /scripts/STARlongMatchAnnot_commands_ENCODE_den...
Snapshots: Snapshot 1
Assay: _A_02.6_TransRate Short Name: 02.6_TransRate Assay Class: DRY Assay Type: TransRate Title: TransRate stat on raw tr2aacds transcriptomes Description: TransRate stat on raw (initial) tr2aacds transcriptomes, basic and reference-based pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Nonde Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Validation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar
Snapshots: Snapshot 1
Assay: _A_02.7_VecScreen Short Name: 02.7_VecScreen Assay Class: DRY Assay Type: VecScreen Title: VecScreen on raw tr2aacds output Description: VecScreen (contamination screening) and blastn (contaminants annotation) on raw (initial) tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Validation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum, Potato virus Y
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /intermediate.tar.gz, /output/Desiree_vecscreen.tsv, /output/PW363_vecscreen.tsv, /output/Rywal_vecscreen.tsv, /scripts/01_get_input.sh, /scripts/02_VecScreenPlus_blastn.sh, /scripts/ENCH_sumablastplus.pl
Snapshots: Snapshot 1
Assay: _A_02.8_DIAMOND Short Name: 02.8_DIAMOND Assay Class: DRY Assay Type: DIAMOND Title: DIAMOND on raw tr2aacds output Description: DIAMOND on raw tr2aacds output, both .cds and .tr; including lost and found pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Annotation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar
Snapshots: Snapshot 1
Abstract (Expand)
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