Assay:	_A_AgroinfFinalConstructsdCas9EV-GCMS
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 guide was made in pLX vector so it could be co-transformed in the same agrobacterium colony with the moth pheromone pathway. Such Agrobacterium containing both plasmids (guided/nonguided pathway + nonguided/guided copper-inducible dCas9EV) was agroinfiltrated before stable transformation in Nicotiana benthamiana to check the expression of the genes.
pISA Assay creation date:	2021-05-03
pISA Assay creator:	ElenaMG
Lab manager:	DO
Sample collection protocol:	Leaf samples were collected at 5 days post-infiltration, frozen in liquid nitrogen immediately, and ground afterwards.
Extraction protocol:	50mg of frozen, ground leaf samples were weighed in a 10mL headspace screw-cap vial and stabilized by adding 1mL of 5M CaCl2 and 150 μL of 500mM EDTA (pH = 7.5), after which they were sonicated for 5 minutes. Volatile compounds were captured by means of headspace solid phase microextraction (HS-SPME) with a 65 μm polydimethylsiloxane/divinylbenzene (PDMS/DVB) SPME fiber (Supelco, Bellefonte, PA, USA). Volatile extraction was performed automatically by means of a CombiPAL autosampler (CTC Analytics). Vials were first incubated at 80°C for 3 minutes with 500 rpm agitation. The fiber was then exposed to the headspace of the vial for 20 min under the same conditions of temperature and agitation. Desorption was performed at 250°C for 1 minute (splitless mode) in the injection port of a 6890N gas chromatograph coupled to a 5975B mass spectrometer (Agilent Technologies). After desorption, the fiber was cleaned in a SPME fiber conditioning station (CTC Analytics) at 250°C for 5 min under a helium flow.
Chromatography protocol:	Chromatography was performed on a DB5ms (60 m, 0.25 mm, 1 μm) capillary column (JandW) with helium as the carrier gas at a constant flow of 1.2mLxmin-1. The oven programming conditions were an initial temperature of 160°C for 2 min, 7°Cmin-1 ramp until 280°C, and a final hold at 280°C for 6 minutes to reduce the overall running time without losing resolution of the desired compounds.
Mass spectrometry protocol:	Electron impact ionization (EI), 70 eV ionization energy, MS source temperature 230ºC, MS quadrupole temperature 150ºC, single quadrupole detector, m/z range 35-300.
Phenodata:	../../phenodata_20210107
Featuredata:	
Creation date:	2021-05-03
Extract ID:	$_extr
Extraction Method:	HS-SPME
Date Extraction:	2021-05-03
Derivatization or Labelling:	none
Date Derivatization or Labelling:	2021-05-03
Derivatized or labeled Extract ID:	$_extrD
Other Post Extraction Procedures:	
Storage:	
Date GC-MS Run:	2021-05-03
GC Instrument:	6890N gas chromatograph (Agilent Technologies)
GC Autosampler Model:	CombiPAL autosampler (CTC Analytics)
GC Column model:	DB5ms (60m, 0.25 mm, 1um) capillary column (JandW)
GC Column type:	capillary column
Guard Column:	
MS Scan polarity:	positive
MS Scan mz range:	35-300
MS Instrument:	5975B mass spectrometer (Agilent Technologies)
MS Ion source:	electron ionization (EI)
Mass analyzer:	quadrupole mass filter
Operator:	ElenaMG
Notes:	
Data:	https://doi.org/10.5281/zenodo.5810197