_S_04_Stages

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Short Name: 04_Stages Title: Expression of target genes in CPB developmental stages and body parts Description: Expression of target genes in CPB developmental stages and body parts Raw Data: pISA Study creation date: 2021-05-10 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/398

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 (4)
Data files (36)
Documents (31)

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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_04_Stages-files

_p_RNAinVAL

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Andrej Blejec

Files connected to study: _S_04_Stages

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_04_Stages

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_02_qPCR_ampl_test-wet

_p_RNAinVAL

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Andrej Blejec

Short Name: 02_qPCR_ampl_test-wet Assay Class: WET Assay Type: wet Title: Test of qPCR amplicons Description: Test of qPCR ampliconed designed to follow expression of target genes pISA Assay creation date: 2021-05-10 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_04_Stages

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/05132016_RNAinVAL_amplicon_test_results...., output/05172016_RNAinVAL_amplicon_test2_results..., output/RNAinVAL_amplicon_REtest_384_05172016.xlsx, output/RNAinVAL_amplicon_test_384_05132016.xlsx, output/raw/05132016_JHBP_TqMn.txt, output/raw/05132016_alas.txt, output/raw/05132016_mesh.txt, output/raw/05132016_vATPaseE.txt, output/raw/alas.txt

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Created: 10th Nov 2021 at 09:34, Last updated: 10th Nov 2021 at 15:22

_A_03_stages-RNAisol

_p_RNAinVAL

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Andrej Blejec

Short Name: 03_stages-RNAisol Assay Class: WET Assay Type: RNAisol Title: Expression of target genes in CPB developmental stages and body parts Description: Expression of target genes in CPB developmental stages and body parts - RNA isolation pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Lab manager: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: RNA ID: $_RNA Homogenisation protocol: handheld electric rotor-stator homogenization in tubes with Trizol Date ...

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_04_Stages

Organisms: No organisms

SOPs: No SOPs

Snapshots: No snapshots

Created: 10th Nov 2021 at 09:34, Last updated: 10th Nov 2021 at 11:28

_A_04_stages-qPCR

_p_RNAinVAL

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Andrej Blejec

Short Name: 04_stages-qPCR Assay Class: WET Assay Type: qPCR Title: qPCR of stages samples Description: qPCR of stages samples for target genes pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: Data: Lab manager: Kristina Gruden Assay chemistry: mixed Assay optimisation protocol (file path, link or citation): Pippeting: liquid handling station and manual Reaction volume: 5 ul qPCR platform: HT7900 Fast, ABI (SDS); Viia7, ABI ...

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_04_Stages

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, other/DNA_removal_qPCR_18S_mesh_20170118.xlsx, other/phenodata_nonstandarized.xlsx, other/phenodata_stages.xlsx, reports/QUANTGENIUS__experiment_RNAinVAL_CPB_st...

Snapshots: No snapshots

Created: 10th Nov 2021 at 09:34, Last updated: 10th Nov 2021 at 11:28

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output/raw/alas.txt

_p_RNAinVAL

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Andrej Blejec

_p_RNAinVAL/_I_01_LabTrials/_S_04_Stages/_A_02_qPCR_ampl_test-wet/