Assays

Short Name: 01_AgroRNA-wet Assay Class: WET Assay Type: wet Title: Order dsRNA in-vitro synthesis at AgroRNA Description: Materials associated with the order of in-vitro synthesis of designed dsRNA, results of cleaning procedure and DNase I test to ensure the material is not DNA pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

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:

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:

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:

Short Name: 02_jun2017-RNAisol Assay Class: WET Assay Type: RNAisol Title: RNA isolation and pre-qPCR sample prep Description: RNA isolation and sample preparation for qPCR 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 Homogenisation: 2017-07-17 Isolation Protocol: ZymoRNA Date Isolation: ...

Short Name: 00_jun2017_dsRNA_stabil-wet Assay Class: WET Assay Type: wet Title: Stability testing of in-vitro synthetised dsRNA Description: Stability testing by gel electrophoresis before/after DNase and RNase reactions pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Short Name: 02_dec2016-RNAisol Assay Class: WET Assay Type: RNAisol Title: RNA isolation and pre-qPCR sample prep Description: RNA isolation and sample preparation for qPCR 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 Homogenisation: 2017-08-17 Isolation Protocol: ZymoRNA Date Isolation: ...

Short Name: 03_jun2016-qPCR Assay Class: WET Assay Type: qPCR Title: qPCR for target genes Description: Quantitative PCR (qPCR) for selected target genes using the established methodology at NIB. pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: Data: ../../_S_07_dec2016/_A_03-qPCR/output Lab manager: Kristina Gruden Assay chemistry: mixed Assay optimisation protocol (file path, link or citation): Pippeting: liquid handling ...

Short Name: 02_jun2016-RNAisol Assay Class: WET Assay Type: RNAisol Title: RNA isolation and pre-qPCR sample prep Description: RNA isolation and sample preparation for qPCR 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 Homogenisation: 2017-04-26 Isolation Protocol: ZymoRNA Date Isolation: ...

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 ...

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:

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:

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:

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:

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:

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:

Short Name: 01_jun2017-phenotyping Assay Class: WET Assay Type: phenotyping Title: Measuring feeding trial parameters Description: Weight gain, survival, photos and other phenotypic observations pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek, Valentina Levak Phenodata: ../../phenodata_20210113.txt Featuredata: Data:

Files connected to investigation: _I_01_LabTrials

Files connected to study: _S_11_may2018

Files connected to study: _S_10_apr2018

Files connected to study: _S_09_jun2017

Files connected to study: _S_08_jan2017

Files connected to study: _S_07_dec2016

Files connected to study: _S_06_oct2016

Files connected to study: _S_05_jun2016

Files connected to study: _S_04_Stages

Files connected to study: _S_03_dsRNAprod

Files connected to study: _S_02_dsRNAorder

Files connected to study: _S_01_TargetSelect

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