Assays

Short Name: qRTPCRMothPheromonesEnzymes-Q-RT-PCR Assay Class: WET Assay Type: Q-RT-PCR Title: qRT-PCR Analysis of enzymes AtrD11 and HarFar in Penicillium digitatum transformants Description: Two Penicillium digitatum transformants were selected that showed integration of the two genes AtrD11 and HarFar (PCR test) but not moth pheromone production (GC-MS, analysed in CEQA facilities). These two transformants were then assayed in their expression of the transgenes by qRT-PCR. pISA Assay creation ...

Files connected to study: _S_P1_TransgenicStableSxPv2

Short Name: SxPdCasEVNonGuidedPathway-GCMS Assay Class: WET Assay Type: GCMS Title: SxP dCasEV Non Guided Pathway (EV NGP) Description: Generation and analysis of the stable Nicotiana benthamiana transgenic plants with the moth sex pheromone biosynthetic pathway genes regulated by synthetic promotors, the dCasEV system and not provided with the specific guide in stable. The activation of the pathway was performed by agroinfiltration of the specific guide in trans, so the system is complete and ...

Short Name: SxPGuidedPathway-GCMS Assay Class: WET Assay Type: GCMS Title: SxP Guided Pathway (GP) Description: Generation and analysis of the stable Nicotiana benthamiana transgenic plants with the moth sex pheromone biosynthetic pathway genes regulated by synthetic promotors and provided with the specific guide in stable. The purpose of this assay is to measure the volatile moth sex pheromone production by HSPME GCMS of the generated stable Nicotiana benthamiana plants. The activation of the ...

Short Name: SxPNonGuidedPathway-GCMS Assay Class: WET Assay Type: GCMS Title: SxP Non Guided Pathway (NGP) Description: Generation and analysis of the stable Nicotiana benthamiana transgenic plants with the moth sex pheromone biosynthetic pathway genes regulated by synthetic promotors and not provided with the specific guide in stable. The activation of the pathway was performed by agroinfiltration of the dCasEV and the specific guide in trans, so the system is complete and the production of the ...

Files connected to investigation: _I_T22_SxPv2

Files connected to study: _S_P1_TransientExp_Nb

Short Name: AgroinfFinalConstructsdCas9EV-GCMS Assay Class: WET Assay Type: GCMS Title: Agroinfiltration of final constructs for copper-inducible pathway in Nicotiana benthamiana leaves Description: Two constructs were made containing the three genes of the moth pheromone pathway under the regulation of synthetic promoters made in T11, nptII selection marker and with/without the gRNA1 for activation. In parallel, another construct containing the copper-inducible dCas9EV system with/without the ...

Short Name: AgroinfGuidedPathwaywithConstitutivedCas9EV-GCMS Assay Class: WET Assay Type: GCMS Title: Agroinfiltration of guided pathway for moth pheromones production with constitutive dCas9EV system in Nicotiana benthamiana leaves Description: Two constructs were made that comprised the three genes required for moth pheromone production (AtrD11, HarFar and EaDAct/ATF1) under the regulation of the synthetic promoters created in T11. In the constructs it was also included the guideRNA1 and nptII ...

Short Name: AgroinfNonGuidedPathwaywithCopperInducibledCas9EV-GCMS Assay Class: WET Assay Type: GCMS Title: Agroinfiltration of non-guided pathway for moth pheromones production with copper-inducible dCas9EV system in Nicotiana benthamiana leaves Description: Two constructs were made that comprised the three genes required for moth pheromone production (AtrD11, HarFar and EaDAct/ATF1) under the regulation of the synthetic promoters created in T11. The constructs were first tested transiently in ...

Short Name: AgroinfNonGuidedPathwayywithConstitutivedCas9EV-GCMS Assay Class: WET Assay Type: GCMS Title: Agroinfiltration of nonguided pathway for moth pheromones production with constitutive dCAs9EV system in Nicotiana benthamiana leaves Description: Two constructs were made that comprised the three genes required for moth pheromone production (AtrD11, HarFar and EaDAct/ATF1) under the regulation of the synthetic promoters created in T11. The constructs were first tested transiently in Nicotiana ...

Files connected to investigation: _I_T12_CuInducible

Short Name: 20200818-LUM Assay Class: WET Assay Type: LUM Title: Luciferase assay of new minimal promoters Description: New minimal promoters were designed and tested to increase the battery of pieces available for creating synthetic promoters pISA Assay creation date: 2020-08-18 pISA Assay creator: ElenaMG Lab manager: DO Operator: ElenaMG Link to SynBio DM: https://docs.google.com/spreadsheets/d/1KqJ2s7WZOro2pTCjGuUDpnSRfum26omN1TRFDl6-gAI/edit#gid=1915967703 Link to protocols: ../protocols/LUCIFERASE ...

Short Name: 20201112-LUM Assay Class: WET Assay Type: LUM Title: Luciferase assay re-testing US6.X Description: The US6.X series was tested again using separated plasmids for the gRNAs and the dCas9EV system (so far it was used a plasmid containig the system and the guide together) pISA Assay creation date: 2020-11-12 pISA Assay creator: ElenaMG Lab manager: DO Operator: ElenaMG Link to SynBio DM: https://docs.google.com/spreadsheets/d/1KqJ2s7WZOro2pTCjGuUDpnSRfum26omN1TRFDl6-gAI/edit#gid=1915967703 ...

Short Name: 20211221-LUM Assay Class: WET Assay Type: LUM Title: dCasEV synthetic promoters with NanoLuc reporter system Description: Test for dCasEV synthetic promoters using EI reporter system based on Nanoluciferase as reporter and luciferase as reference signal. pISA Assay creation date: 2021-12-22 pISA Assay creator: ElenaMG Lab manager: DO Operator: ElenaMG Link to SynBio DM: https://docs.google.com/spreadsheets/d/1KqJ2s7WZOro2pTCjGuUDpnSRfum26omN1TRFDl6-gAI/edit#gid=1915967703 Link to ...

Short Name: 20190208-LUM Assay Class: WET Assay Type: LUM Title: Luciferase assay first trial Description: Promoter series containing random sequences and the recognition sequence for guideRNA1 DFR (P1.X series) fused to the developed core promoter minDFR and to luciferase for measuring the expression in the presence or absence of such guideRNA1 DFR. A promoter containing the target sequence in a different position (P1.7.1) and a promoter with the target sequence repeated twice (P2.1) were also ...

Short Name: 20190717-LUM Assay Class: WET Assay Type: LUM Title: Luciferase assay second trial Description: New 1.X and P2.X promoter sequences, and also a P3.1 promoter containing three times the target sequence for guideRNA1 DFR pISA Assay creation date: 2019-07-17 pISA Assay creator: ElenaMG Lab manager: DO Operator: ElenaMG Link to SynBio DM: https://docs.google.com/spreadsheets/d/1KqJ2s7WZOro2pTCjGuUDpnSRfum26omN1TRFDl6-gAI/edit#gid=1915967703 Link to protocols: ../protocols/LUCIFERASE ...

Short Name: 20191209-LUM Assay Class: WET Assay Type: LUM Title: Luciferase assay third trial Description: In order to imitate better the native DFR promoter, all upstream promoter sequences were re-designed as A2 pieces and A1 pieces were ordered which consisted on just random sequences witout any promoter signals. Assembling these pieces created synthetic promoters of the same length than the original SlDFR. Due to some assembly issues, all new constructs were made using 35s terminator. pISA ...

Short Name: 20200219-LUM Assay Class: WET Assay Type: LUM Title: Luciferase assay of different A1 random sequences Description: With the aim of making three promoters as different as possible for the moth pheromone enzymes, three A1 pieces containing random sequences withous any promoter signal were assembled and tested using luciferase assay. pISA Assay creation date: 2020-02-19 pISA Assay creator: ElenaMG Lab manager: DO Operator: ElenaMG Link to SynBio DM: ...

Short Name: 20200302-LUM Assay Class: WET Assay Type: LUM Title: Luciferase Assay US1.7.X and US3.X pieces Description: Analysis of new US pieces with three recognition sites for gRNA1 DFR (US3.X) and US pieces with the recognition site in different positions (US1.7.1-US1.7.4), as well as another US part with the recognition site of another gRNA (US1.7.5, for gRNA4 from NOS promoter). pISA Assay creation date: 2020-02-03 pISA Assay creator: ElenaMG Lab manager: DO Operator: ElenaMG Link to SynBio ...

Files connected to investigation: _I_T11_dCas9SynProm

Files connected to study: _S_P1_SynProm_Nbenthamiana

Short Name: 04_mapReadsToAs2-STAR Assay Class: DRY Assay Type: STAR Title: Map RNAseq reads to de-novo assembly2 Description: STAR mapper was used to map back P citri RNAseq reads used for generation the de-novo assembly2. pISA Assay creation date: 2019-05-24 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Short Name: 05_As2_tr_limmaDE-R Assay Class: DRY Assay Type: R Title: Assembly2 transcripts differential expression analysis using limma voom package Description: Using output files of mapReadsToAss2 by STAR the counts were analyzed for differential expression in R using limma voom approach. pISA Assay creation date: 2019-06-19 pISA Assay creator: MPE Analyst: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data: ../_A_04_mapReadsToAs2-STAR/output/*.counts

Files connected to study: _S_P4_Pcitri_tr2

Short Name: 02_CDHIT-Bioinfo Assay Class: DRY Assay Type: Bioinfo Title: Combining tr1 and tr2 using CD-HIT-EST Description: Merging and removing redundant sequences (100% identical or contained) from the merged tr1 and tr2 set pISA Assay creation date: 2021-12-16 pISA Assay creator: MPE Phenodata: None Featuredata: Data:

Short Name: 01_assembly2-rnaSPAdes Assay Class: DRY Assay Type: rnaSPAdes Title: P citri de-novo transcriptome assembly 2 Description: P citri de-novo transcriptome assembly using SUSPHIRE and mealybug.org RNA-seq datasets pISA Assay creation date: 2019-05-24 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Short Name: 02_assembly2-IPS Assay Class: DRY Assay Type: IPS Title: Assembly2 InterProScan Description: InterProScan run for de-novo assembly2 transcripts. AA sequences were obtained by runing transeq and filtering to 3 longest ORFs per transcript. pISA Assay creation date: 2019-05-24 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20190523.txt Featuredata: Data: ../_A_01_assembly2-rnaSPAdes/output/soft_filtered_transcripts.fasta

Short Name: 03_mapAs2ToGenome-STAR Assay Class: DRY Assay Type: STAR Title: Mapping assembly2 transcripts to P citri genome Description: Mapping de novo assembled transcripts from SUSPHIRE and Ediburgh RNA-Seq datasets (assembly2) to P citri genome using STARlong. MatchAnnot also run. pISA Assay creation date: 2019-06-19 pISA Assay creator: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Assay Class: DRY Assay Type: Bioinfo Title: Combining short read de novo transcriptome with IsoSeq Description: After first round of CDHIT to combine both versions of the denovo Pcitri transcriptome, CDHIT was run again to combine it with IsoSeq isoforms and perpare a consolidates transcriptomic sequence resource for P. citri pISA Assay creation date: 2022-07-01 pISA Assay creator: Mojca Jutersek Phenodata: ../../phenodata_20190523.txt Featuredata: Data: Principal investigator: Diego Orzaez ...