Assays

What is an Assay?

13 Assays visible to you, out of a total of 13

_p_stRT

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

Created: 7th Nov 2019 at 15:54, Last updated: 16th Nov 2019 at 13:21

_A_02.7_VecScreen

_p_stRT

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

DOI: 10.15490/fairdomhub.1.assay.1168.1

Created: 7th Nov 2019 at 16:58, Last updated: 16th Nov 2019 at 11:37

Hormone concentrations

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

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

Created: 18th Feb 2019 at 18:59, Last updated: 4th Mar 2019 at 16:51

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

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

Created: 4th Mar 2019 at 15:23, Last updated: 4th Mar 2019 at 16:51

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

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

Created: 18th Feb 2019 at 18:58, Last updated: 4th Mar 2019 at 16:51

sRNAomics (bioinformatics)

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

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

Created: 18th Feb 2019 at 18:56, Last updated: 4th Mar 2019 at 16:51

sRNAomics (qPCR)

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

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

Created: 18th Feb 2019 at 18:55, Last updated: 4th Mar 2019 at 16:51

sRNAomics (sRNA-Seq)

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

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

Created: 18th Feb 2019 at 18:54, Last updated: 4th Mar 2019 at 16:51

Transcriptomics (qPCR)

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

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

Created: 18th Feb 2019 at 18:52, Last updated: 4th Mar 2019 at 16:50

Transcriptomics (microarrays)

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

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

Created: 18th Feb 2019 at 18:51, Last updated: 4th Mar 2019 at 16:50

Pathogen abundance

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

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

Created: 18th Feb 2019 at 18:49, Last updated: 4th Mar 2019 at 16:50

Photosynthetic activity

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

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

Created: 18th Feb 2019 at 18:47, Last updated: 4th Mar 2019 at 16:50

Disease symptoms

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

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

Created: 18th Feb 2019 at 18:43, Last updated: 4th Mar 2019 at 16:49

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