Summary of Study ST001879

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001185. The data can be accessed directly via it's Project DOI: 10.21228/M8J407 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST001879
Study Title	Proteomics reveals an increase in the abundance of glycolytic and ethanolic fermentation enzymes in developing sugarcane culms during sucrose accumulation
Study Summary	Sugarcane is an economically important crop contributing to the world’s sugar and ethanol production with 80% and 40%, respectively. Metabolites from I5-4M and I9-4M were extracted from six biological samples of four-month-old plants. Following the removal of leaves, the internodes were identified and cut, and the bark removed, and the remaining tissue was immediately frozen in liquid nitrogen.
Institute	ESALQ-USP
Department	Genetics
Laboratory	Laboratório Max Feffer de Genética de Plantas
Last Name	Cataldi
First Name	Thais
Address	Padua Dias Avenue, 11, Piracicaba, São Paulo, 13418-900, Brazil
Email	thais.cataldi@usp.br
Phone	+551934294248
Submit Date	2021-07-19
Raw Data Available	Yes
Raw Data File Type(s)	cdf
Analysis Type Detail	GC-MS
Release Date	2022-02-16
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001185
Project DOI:	doi: 10.21228/M8J407
Project Title:	Proteomics reveals an increase in the abundance of glycolytic and ethanolic fermentation enzymes in developing sugarcane culms during sucrose accumulation
Project Type:	Untargeted GC-MS
Project Summary:	GC-MS based approach studies on sugarcane (Saccharum spp) internode development.
Institute:	ESALQ-USP
Department:	Genetics
Laboratory:	Laboratório Max Feffer de Genética de Plantas
Last Name:	Cataldi
First Name:	Thaís
Address:	Padua Dias Avenue, 11
Email:	thais.cataldi@usp.br
Phone:	1934294248
Funding Source:	CAPES, FAPESP

Subject:

Subject ID:	SU001956
Subject Type:	Plant
Subject Species:	Saccharum spp

Factors:

Subject type: Plant; Subject species: Saccharum spp (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment
SA174909	210514_IJ1colmo_1.cdf	I5_4M
SA174910	210514_IJ6colmo_1.cdf	I5_4M
SA174911	210514_IJ5colmo_1.cdf	I5_4M
SA174912	210514_IJ2colmo_1.cdf	I5_4M
SA174913	210514_IJ3colmo_1.cdf	I5_4M
SA174914	210514_IJ4colmo_1.cdf	I5_4M
SA174915	20210513_ColmIM6_1.cdf	I9_4M
SA174916	20210513_ColmIM5_1.cdf	I9_4M
SA174917	20210513_ColmIM1_1.cdf	I9_4M
SA174918	20210513_ColmIM2_1_1.cdf	I9_4M
SA174919	20210513_ColmIM3_1.cdf	I9_4M
SA174920	20210513_ColmIM4_1.cdf	I9_4M

Showing results 1 to 12 of 12

Showing results 1 to 12 of 12

Collection:

Collection ID:	CO001949
Collection Summary:	Sugarcane internodes (I5 and I9) from 4 month-old plants were harvested and frozen in liquid nitrogen.
Sample Type:	Plant

Treatment:

Treatment ID:	TR001968
Treatment Summary:	Sugarcane cultivar SP80-3280 was grown in greenhouse conditions, at Piracicaba, São Paulo, Brazil (22°43’31’’S; 47°38’57’’W). Culms with one bud were planted in plastic trays and after acclimatization for two months, nine plants were transferred to 100 L plastic pots, containing soil (latosol). The temperature in the greenhouse was automatically adjusted to 28ºC ± 1ºC and 12/12 h light/dark photoperiod. Plants were watered to maintain soil capacity once a day, in the morning. Fertilizer was supplied once a week using a commercial fertilizer (Plant Prod®, N 15: P2O5 15: K2O 30, Plant Products CO. Canada) at the rate of 2 L per pot (4g/L). The replicates, distributed in a randomized design, were harvest at 4 month-old. During harvest, leaves were excised from the main culm and the internodes 5 and 9 from each plant, were separated and peeled from the top towards the base. Each individual internode was frozen in liquid nitrogen and kept at -80ºC. Six biological replicates from each internode were harvested.

Treatment ID:

TR001968

Treatment Summary:

Sugarcane cultivar SP80-3280 was grown in greenhouse conditions, at Piracicaba, São Paulo, Brazil (22°43’31’’S; 47°38’57’’W). Culms with one bud were planted in plastic trays and after acclimatization for two months, nine plants were transferred to 100 L plastic pots, containing soil (latosol). The temperature in the greenhouse was automatically adjusted to 28ºC ± 1ºC and 12/12 h light/dark photoperiod. Plants were watered to maintain soil capacity once a day, in the morning. Fertilizer was supplied once a week using a commercial fertilizer (Plant Prod®, N 15: P2O5 15: K2O 30, Plant Products CO. Canada) at the rate of 2 L per pot (4g/L). The replicates, distributed in a randomized design, were harvest at 4 month-old. During harvest, leaves were excised from the main culm and the internodes 5 and 9 from each plant, were separated and peeled from the top towards the base. Each individual internode was frozen in liquid nitrogen and kept at -80ºC. Six biological replicates from each internode were harvested.

Sample Preparation:

Sampleprep ID:	SP001962
Sampleprep Summary:	Metabolites from I5-4M and I9-4M were extracted from six biological samples of four-month-old plants. Following the removal of leaves, the internodes were identified and cut, and the bark removed (see supplementary figure S2), and the remaining tissue was immediately frozen in liquid nitrogen. Prior to metabolite extraction frozen internode tissue (100 mg) was grounded under liquid nitrogen using a vibration mill (MM 301 Retch GmbH & Co, Haan, Germany) set to a frequency of 30 Hz s-1 for 45 s, with pre-chilled holders and 3 mm tungsten beads. Internode metabolites were extracted by adding 500 μl of pre-chilled methanol (MeOH): chloroform (CHCl3): water (H20) (6:2:2 v/v/v). The extract was vortexed vigorously, sonicated at 40 Hz s-1 for 15 min and centrifuged at 14.000 x g (Eppendorf Centrifuge 5415R) for 10 min at 4°C. The supernatant was filtered (Millipore filter PVDF 0.22 μm) and 100 μl of each sample was transferred to vials and evaporated until dryness. Samples were derivatized according to Gullberg et al. (2004) with 30 μl of methoxyamine hydrochloride (15 mg ml-1) in pyridine for 16 h at room temperature. The samples were trimethylsilylated by adding 30 μl of N-methyl-N- (trimethylsilyl) trifluoroacetamide (MSTFA) containing 1% trimethylchlorosilane (TMCS), the resulting mixture stand at room temperature for 1 h. After silylation, 30 μl of heptane was added. Stable isotope reference compounds [1 mg ml-1 each of (13C3)-myristic acid, (13C4)-palmitic acid and (2H4)-succinic acid] were added in samples prior to derivatization and used as external standard for quality control. Derivatized samples were analyzed according to Gullberg et al. (2004). Blank control samples and a series of n-alkanes (C12–C40), which allowed retention indices to be calculated (Schauer et al., 2005) were also used.

Sampleprep ID:

SP001962

Sampleprep Summary:

Metabolites from I5-4M and I9-4M were extracted from six biological samples of four-month-old plants. Following the removal of leaves, the internodes were identified and cut, and the bark removed (see supplementary figure S2), and the remaining tissue was immediately frozen in liquid nitrogen. Prior to metabolite extraction frozen internode tissue (100 mg) was grounded under liquid nitrogen using a vibration mill (MM 301 Retch GmbH & Co, Haan, Germany) set to a frequency of 30 Hz s-1 for 45 s, with pre-chilled holders and 3 mm tungsten beads. Internode metabolites were extracted by adding 500 μl of pre-chilled methanol (MeOH): chloroform (CHCl3): water (H20) (6:2:2 v/v/v). The extract was vortexed vigorously, sonicated at 40 Hz s-1 for 15 min and centrifuged at 14.000 x g (Eppendorf Centrifuge 5415R) for 10 min at 4°C. The supernatant was filtered (Millipore filter PVDF 0.22 μm) and 100 μl of each sample was transferred to vials and evaporated until dryness. Samples were derivatized according to Gullberg et al. (2004) with 30 μl of methoxyamine hydrochloride (15 mg ml-1) in pyridine for 16 h at room temperature. The samples were trimethylsilylated by adding 30 μl of N-methyl-N- (trimethylsilyl) trifluoroacetamide (MSTFA) containing 1% trimethylchlorosilane (TMCS), the resulting mixture stand at room temperature for 1 h. After silylation, 30 μl of heptane was added. Stable isotope reference compounds [1 mg ml-1 each of (13C3)-myristic acid, (13C4)-palmitic acid and (2H4)-succinic acid] were added in samples prior to derivatization and used as external standard for quality control. Derivatized samples were analyzed according to Gullberg et al. (2004). Blank control samples and a series of n-alkanes (C12–C40), which allowed retention indices to be calculated (Schauer et al., 2005) were also used.

Combined analysis:

Analysis ID	AN003039
Analysis type	MS
Chromatography type	GC
Chromatography system	Agilent 7890A
Column	Agilent DB5 (20m x 0.18 mm i.d. x 0.18 μm)
MS Type	EI
MS instrument type	GC x GC-TOF
MS instrument name	Leco Pegasus 4D GCxGC TOF
Ion Mode	UNSPECIFIED
Units	relative intensity

Chromatography:

Chromatography ID:	CH002254
Chromatography Summary:	One microliter of each derivatized sample was injected splitless into a gas chromatograph 7890A (Agilent Technologies, Santa Clara, USA) coupled with a Comb-xt Autosampler (Leap Technologies, Carrboro, USA). A 20m x 0.18 mm i.d. x 0.18 μm film thickness, DB5 GC capillary column (Agilent Technologies) was used as the primary column and the secondary GC columns was a 0.69 m x 0.1 mm i.d. x 0.1 μm film thickness (Rxi-17 Restek, Bellefonte, USA). The injector temperature was 280°C, the septum purge flow rate was 20 ml min-1 and the purge was turned on after 60 s. The gas helium flow rate through the column was 1 ml min-1, the column temperature was held at 80°C for 2 min, then increased by 15°C min-1 to 305°C, and held there for 10 min.
Instrument Name:	Agilent 7890A
Column Name:	Agilent DB5 (20m x 0.18 mm i.d. x 0.18 μm)
Chromatography Type:	GC

MS:

MS ID:	MS002829
Analysis ID:	AN003039
Instrument Name:	Leco Pegasus 4D GCxGC TOF
Instrument Type:	GC x GC-TOF
MS Type:	EI
MS Comments:	The column effluent was introduced into the ion source of a GC×GC/TOF-MS (Pegasus 4D, Leco Corp., St. Joseph, USA). The transfer line and the ion source temperatures were 280 and 250°C, respectively. Ions were generated by a 70-eV electron beam at an ionization current of 2.0 mA, and 10 spectra s-1 were recorded in the mass range m/z 45–800. The ChromaTOF software v. 4.51 (Leco Corp., St. Joseph, USA) was used to perform baseline correction, deconvolution, peak detection, retention time alignment and library matching. NIST mass spectral library was used to metabolite identification. Multivariate (Partial least squares-discriminant analysis, PLS-DA) and univariate (t-test, FDR adjusted p ≤ 0.05) analysis were done in MetaboAnalyst 5.0 (Xia et al., 2015). To reduce systematic variance and to improve the performance for downstream statistical analysis data were log-transformed and auto-scaled prior to data analysis. Metabolites detected in at least three replicates in one group (I5 or I9) and not identified in any replicate of the other group were named “exclusive” metabolites.
Ion Mode:	UNSPECIFIED