_S_03_dsRNAprod

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Short Name: 03_dsRNAprod Title: Production of selected desigend dsRNAs in-vivo Description: We established the production of two selected designed dsRNAs in-vivo in bacterial cultures of E. coli TH115 (DE3), a strain that does not produce RNases and is thus suitable for production of long dsRNA Raw Data: pISA Study creation date: 2021-01-14 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/397

Investigation: _I_01_LabTrials

Projects: _p_RNAinVAL

Study position:

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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 (6)
Data files (11)
Documents (55)

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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_03_dsRNAprod-files

_p_RNAinVAL

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Andrej Blejec

Files connected to study: _S_03_dsRNAprod

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_03_dsRNAprod

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_00_Ecoli-dry

_p_RNAinVAL

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Andrej Blejec

Short Name: 00_Ecoli-dry Assay Class: DRY Assay Type: dry Title: E coli HT115 data Description: Information on E coli bacteria used for dsRNA production 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_03_dsRNAprod

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT

Snapshots: No snapshots

Created: 10th Nov 2021 at 09:33, Last updated: 10th Nov 2021 at 11:26

_A_01_pIsol-wet

_p_RNAinVAL

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Andrej Blejec

Short Name: 01_pIsol-wet Assay Class: WET Assay Type: wet Title: Plasmid isolation from bacterial culture Description: Plasmids were obtained as bacterial culture from Addgene and isolated to be used for cloning 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_03_dsRNAprod

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 10th Nov 2021 at 09:33, Last updated: 10th Nov 2021 at 15:12

_A_02_plasmid-SangerSeq

_p_RNAinVAL

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Andrej Blejec

Short Name: 02_plasmid-SangerSeq Assay Class: WET Assay Type: SangerSeq Title: Sanger sequencing of Addgene plasmids Description: Sanger sequencing of Addgene plasmids 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_03_dsRNAprod

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT

Snapshots: No snapshots

Created: 10th Nov 2021 at 09:34, Last updated: 10th Nov 2021 at 15:20

_A_03_RNaseItreat-wet

_p_RNAinVAL

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Andrej Blejec

Short Name: 03_RNaseItreat-wet Assay Class: WET Assay Type: wet Title: RNase If treatment of dsRNA Description: RNase If treatment of dsRNA produced in-vivo 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_03_dsRNAprod

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT

Snapshots: No snapshots

Created: 10th Nov 2021 at 09:34, Last updated: 10th Nov 2021 at 11:26

_A_04_prod-qPCR

_p_RNAinVAL

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Andrej Blejec

Short Name: 04_prod-qPCR Assay Class: WET Assay Type: qPCR Title: qPCR for quantification of dsRNA production in E coli Description: qPCR for quantification of dsRNA production in E coli 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_03_dsRNAprod

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, other/qPCR_Ecoli_16S_GFP_Mesh_20180327.xlsx, output/markop27-03-2018.txt, output/markop27-03-2018.xlsx, reports/quantGenius__16S_MGB_reference_gene.xlsx, reports/quantGenius__dsGFP_L4440_SYBR_target_ge..., reports/quantGenius__dsMesh_SYBR_target_gene.xlsx

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Created: 10th Nov 2021 at 09:34, Last updated: 10th Nov 2021 at 15:20

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reports/quantGenius__dsMesh_SYBR_target_gene.xlsx

_p_RNAinVAL

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Andrej Blejec

_p_RNAinVAL/_I_01_LabTrials/_S_03_dsRNAprod/_A_04_prod-qPCR/