_S_01_TargetSelect

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Short Name: 01_TargetSelect Title: Search for genes that might be good targets for control using dsRNAs (RNAi pesticides) Description: We will examine the results of RNAi screening experiments in model organisms (e.g. Drosophila melanogaster, Tribolium castaneum) as well as employ our previous data and literature knowledge on CPB gene expression and physiology Raw Data: pISA Study creation date: 2021-01-13 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

SEEK ID: https://testing.sysmo-db.org/studies/395

Investigation: _I_01_LabTrials

Projects: _p_RNAinVAL

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Creators and Submitter

Creator

Andrej Blejec

Submitter

Andrej Blejec

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Created: 9th Nov 2021 at 20:41

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People (1)
Programmes (1)
Projects (1)
Investigations (1)
Assays (9)
Data files (63)
Documents (68)

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Andrej Blejec

Institutions: National Institute of Biology, NIB, <script>alert('xss-institution-title')</script> & Test Institution

https://orcid.org/0000-0001-7484-6031

Expertise: STatistics, R, Programming, Data Management

Tools: R, API

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pISA-tree

Local data management; testing uploading/downloading using API

Web page: Not specified

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_p_RNAinVAL

Test upload using seekr before upload to FAIRDOMHub

Programme: pISA-tree

Public web page: Not specified

Organisms: Not specified

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_I_01_LabTrials

_p_RNAinVAL

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Andrej Blejec

Short Name: 01_LabTrials Title: Laboratory trials Description: Selection of targets and their validation in trials performed in the laboratories and greenhouse at NIB Phenodata: ./phenodata_20210113.txt pISA Investigation creation date: 2021-01-13 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Submitter: Andrej Blejec

Studies: Investigation files, _S_01_TargetSelect, _S_02_dsRNAorder, _S_03_dsRNAprod, _S_04_Stages, _S_05_jun2016, _S_06_oct2016, _S_07_dec2016, _S_08_jan2017, _S_09_jun2017, _S_10_apr2018, _S_11_may2018

Assays: _A_00_Ecoli-dry, _A_00_dsRNA_stabil-wet, _A_01-phenotyping, _A_01-phenotyping, _A_01-phenotyping, _A_01-phenotyping, _A_01-phenotyping, _A_01_AgroRNA-wet, _A_01_LitData-dry, _A_01_pIsol-wet, _A_02-RNAisol, _A_02-RNAisol, _A_02-RNAisol, _A_02_UlrichTop100-BLAST, _A_02_plasmid-SangerSeq, _A_02_qPCR_ampl_test-wet, _A_03-qPCR, _A_03-qPCR, _A_03-qPCR, _A_03_RNaseItreat-wet, _A_03_patentDB-BLAST, _A_03_stages-RNAisol, _A_04_ortho-BLAST, _A_04_prod-qPCR, _A_04_stages-qPCR, _A_05_CPB_gene-annot, _A_06_splitter_BLAST-dry, _A_07_MergeEvi-dry, _A_08_SelTargetsA-dry, _I_01_LabTrials-files, _S_01_TargetSelect-files, _S_02_dsRNAorder-files, _S_03_dsRNAprod-files, _S_04_Stages-files, _S_05_jun2016-files, _S_06_oct2016-files, _S_07_dec2016-files, _S_08_jan2017-files, _S_09_jun2017-files, _S_10_apr2018-files, _S_11_may2018-files

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Created: 9th Nov 2021 at 20:41

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_S_01_TargetSelect-files

_p_RNAinVAL

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Andrej Blejec

Files connected to study: _S_01_TargetSelect

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_01_TargetSelect

Organisms: No organisms

SOPs: No SOPs

Data files: _STUDY_METADATA.TXT

Snapshots: No snapshots

Created: 9th Nov 2021 at 20:41, Last updated: 9th Nov 2021 at 20:41

_A_01_LitData-dry

_p_RNAinVAL

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Andrej Blejec

Short Name: 01_LitData-dry Assay Class: DRY Assay Type: dry Title: Compiling literature data on RNAi screens in insects Description: Compiling articles and final results of insect RNAi screens in model organisms (e.g. Drosophila melanogaster, Tribolium castaneum) pISA Assay creation date: 2021-01-13 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_01_TargetSelect

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/Dm_mart_export.xls, output/GenomeRNAi_v14_FrequentHitters/GenomeRNA..., output/GenomeRNAi_v14_FrequentHitters/GenomeRNA..., output/Schnorrer_2010_Dm/Dm_lethal phenotypes n..., output/Schnorrer_2010_Dm/publication_info.txt, output/Tc-Ld-rnai_targets based on Tribolum.txt, output/Tc_mart_export.xls, output/Tenerius_2011/Terenius 2011 mmc2.xls, output/Tenerius_2011/publication_info.txt, output/Ulrich_2015/biomart-Ulrich2015_top100Dm.xls, output/Ulrich_2015/publication_info.txt, output/Ulrich_2015/uniprot-Ulrich2015_top100Tc.xls, output/human proteome turnover 2012 mcp.M111.01..., output/iBeetle_Tc/iB2Tc.csv, output/iBeetle_Tc/iB2Tc.xlsx, output/iBeetle_Tc/iBeetle-Base_larva_80penetran..., output/publication_info.txt

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Created: 9th Nov 2021 at 21:02, Last updated: 10th Nov 2021 at 13:58

_A_02_UlrichTop100-BLAST

_p_RNAinVAL

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Andrej Blejec

Short Name: 02_UlrichTop100-BLAST Assay Class: DRY Assay Type: BLAST Title: BLAST Ulrich top100 hits from Tribolium against CPB Description: Analysis of BLAST results from a query of top100 differentially expressed genes of Tribolium castaneum against Colorado potato beetle transcripts pISA Assay creation date: 2021-01-13 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_01_TargetSelect

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/Tctop100cds__CPB_genome_nucl.tsv, output/Tctop100cds__CPB_genome_nucl.xlsx, output/Tctop100cds__CPB_genome_prot.tsv, output/Tctop100cds__CPB_genome_prot.xlsx, output/Tctop100cds__Ld_nucl.tsv, output/Tctop100cds__Ld_nucl.xlsx, scripts/ablastplus_shell_execution.txt

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Created: 9th Nov 2021 at 21:02, Last updated: 10th Nov 2021 at 09:37

_A_03_patentDB-BLAST

_p_RNAinVAL

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Andrej Blejec

Short Name: 03_patentDB-BLAST Assay Class: DRY Assay Type: BLAST Title: NCBI patent BLAST Description: This is to find CPB nucleotide and peptide sequences that are already protected by patents pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_01_TargetSelect

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/aa/160128-markop-741.tsv, output/nt/160128-markop-740.tsv

Snapshots: No snapshots

Created: 10th Nov 2021 at 09:33, Last updated: 10th Nov 2021 at 13:53

_A_04_ortho-BLAST

_p_RNAinVAL

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Andrej Blejec

Short Name: 04_ortho-BLAST Assay Class: DRY Assay Type: BLAST Title: BLAST to determine orthologs to model organisms Description: BLAST against D melanogaster and T castaneum to identify putative orthologous genes of CPB pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_01_TargetSelect

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/LDEC_Dm_orthologs.tsv, output/LDEC_Tc_orthologs.tsv

Snapshots: No snapshots

Created: 10th Nov 2021 at 09:33, Last updated: 10th Nov 2021 at 09:37

_A_05_CPB_gene-annot

_p_RNAinVAL

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Andrej Blejec

Short Name: 05_CPB_gene-annot Assay Class: DRY Assay Type: annot Title: CPB gene annotation using Blast2GO Description: Annotation of CPB predicted genes/proteins using Blast2GO (B2G) suite pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_01_TargetSelect

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/Control vs. PVY-reared vs. Healthy-reare..., output/blast2go_go_table_20160405_0851.txt, output/blast2go_go_table_20160405_0851.xlsx

Snapshots: No snapshots

Created: 10th Nov 2021 at 09:33, Last updated: 10th Nov 2021 at 15:13

_A_06_splitter_BLAST-dry

_p_RNAinVAL

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Andrej Blejec

Short Name: 06_splitter_BLAST-dry Assay Class: DRY Assay Type: dry Title: Split transcripts and BLAST short fragments against insect genomes Description: Split CPB transcripts predicted from the genome into fragments of 21 nt using EMBOSS splitter program and BLASTn againt transcripts of selected insect genomes pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_01_TargetSelect

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/BLAST/LDEC_mRNA_splitter.tsv, reports/LDEC_mRNA_splitter.xlsx, scripts/splitter_BLAST_commands.txt

Snapshots: No snapshots

Created: 10th Nov 2021 at 09:33, Last updated: 10th Nov 2021 at 15:09

_A_07_MergeEvi-dry

_p_RNAinVAL

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Andrej Blejec

Short Name: 07_MergeEvi-dry Assay Class: DRY Assay Type: dry Title: Merge evidence from previous assays for CPB genome Description: Merge all evidence from literature, databases and BLAST results for target gene selection pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_01_TargetSelect

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, reports/12864_2015_1880_MOESM1_ESM Top100 Tc RN...

Snapshots: No snapshots

Created: 10th Nov 2021 at 09:33, Last updated: 10th Nov 2021 at 10:38

_A_08_SelTargetsA-dry

_p_RNAinVAL

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Andrej Blejec

Short Name: 08_SelTargetsA-dry Assay Class: DRY Assay Type: dry Title: Bioinformatics analyses for individual selected target genes Description: In depth bioinformatic analysis for each target gene using various tools to predict possible off-target effects and select a fragment sequence for dsRNA synthesis pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_01_TargetSelect

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, input/12864_2015_1880_MOESM1_ESM Top100 Tc RNAi..., other/NotInFinalSelection/Actin_genome-mRNA_Nuc..., other/NotInFinalSelection/smt3_dsRNA_region.txt, other/NotInFinalSelection/smt3_dsRNA_region_spl..., output/ALAS/Alas_blastn_Human_RefSeq_mRNA-HitTa..., output/ALAS/Alas_dsRNA_region.txt, output/ALAS/Alas_dsRNA_region_splitter.tsv, output/EGFP/Egfp_dsRNA_region.txt, output/EGFP/Egfp_dsRNA_region_splitter.tsv, output/JHBP/JHBP-like_blastn_Human_RefSeq_mRNA-..., output/JHBP/JHBP-like_dsRNA_region.txt, output/JHBP/JHBP-like_dsRNA_region_splitter.tsv, output/JHBP/JHBP-like_dsRNA_region_splitter_Ref..., output/MESH/Mesh_blastn_Human_RefSeq_mRNA-HitTa..., output/MESH/Mesh_mRNA.txt, output/MESH/Mesh_mRNA_splitter.tsv, reports/order_primers_dsRNA_syn/Order_primers&p..., reports/order_primers_dsRNA_syn/ordered_primers..., scripts/splitter_ablast_commands.txt

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Created: 10th Nov 2021 at 09:33, Last updated: 10th Nov 2021 at 15:11

Showing 20 out of a possible 63 Data files Advanced Data files list for this Study with search and filtering

reports/order_primers_dsRNA_syn/ordered_primers_dilutions.xlsx

_p_RNAinVAL

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Andrej Blejec

_p_RNAinVAL/_I_01_LabTrials/_S_01_TargetSelect/_A_08_SelTargetsA-dry/