Summary of Study ST003329

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 PR002071. The data can be accessed directly via it's Project DOI: 10.21228/M8X835 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	ST003329
Study Title	Effect of the serine/arginine-rich (SR) protein RSP-6 overexpression (OE) under the low mTORC1 activity on metabolism in Caenorhabditis elegans
Study Summary	Cellular growth and organismal development are remarkably complex processes that require the nutrient-responsive kinase mechanistic target of rapamycin complex 1 (mTORC1). Anticipating that important mTORC1 functions remained to be identified, we employed genetic and bioinformatic screening in C. elegans to uncover mechanisms of mTORC1 action. Here we show that during larval growth nutrients induce an extensive reprogramming of gene expression and alternative mRNA splicing by acting through mTORC1. mTORC1 regulates mRNA splicing and production of protein-coding mRNA isoforms largely independently of its target p70S6K, by increasing the activity of the serine/arginine-rich (SR) protein RSP-6 (SRSF3/7) and other splicing factors. mTORC1-mediated mRNA splicing regulation is critical for growth, mediates nutrient control of mechanisms that include energy, nucleotide, amino acid, and other metabolic pathways, and may be conserved in humans. Although mTORC1 inhibition delays aging, mTORC1-induced mRNA splicing promotes longevity, suggesting that when mTORC1 is inhibited enhancement of this splicing might provide additional anti-aging benefits.
Institute	Hiroshima University
Last Name	Ogawa
First Name	Takafumi
Address	1-3-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8530, Japan
Email	takafumi-ogawa@hiroshima-u.ac.jp
Phone	+81-80-9790-5278
Submit Date	2024-07-17
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2025-07-17
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002071
Project DOI:	doi: 10.21228/M8X835
Project Title:	Nutrient control of growth and metabolism through mTORC1 regulation of mRNA splicing
Project Summary:	Steady-state non-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) was carried out on Caenorhabditis elegans that overexpress RSP-6 and were treated with Empty Vector (EV) or raga-1 RNAi at the L1 larval stage.
Institute:	Hiroshima University
Last Name:	Ogawa
First Name:	Takafumi
Address:	1-3-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8530, Japan
Email:	takafumi-ogawa@hiroshima-u.ac.jp
Phone:	+81-80-9790-5278

Subject:

Subject ID:	SU003450
Subject Type:	Invertebrate
Subject Species:	Caenorhabditis elegans
Taxonomy ID:	6239
Age Or Age Range:	L1 larva stage
Species Group:	Invertebrates

Factors:

Subject type: Invertebrate; Subject species: Caenorhabditis elegans (Factor headings shown in green)

mb_sample_id	local_sample_id	Genotype	Treatment
SA362409	ctrl_EV_1	rol-6 transgene control animal	empty vector
SA362410	ctrl_EV_2	rol-6 transgene control animal	empty vector
SA362411	ctrl_EV_3	rol-6 transgene control animal	empty vector
SA362412	ctrl_raga1_1	rol-6 transgene control animal	raga-1
SA362413	ctrl_raga1_2	rol-6 transgene control animal	raga-1
SA362414	ctrl_raga1_3	rol-6 transgene control animal	raga-1
SA362403	RSP6OE_EV_1	RSP-6 overexpression	empty vector
SA362404	RSP6OE_EV_2	RSP-6 overexpression	empty vector
SA362405	RSP6OE_EV_3	RSP-6 overexpression	empty vector
SA362406	RSP6OE_raga1_1	RSP-6 overexpression	raga-1
SA362407	RSP6OE_raga1_2	RSP-6 overexpression	raga-1
SA362408	RSP6OE_raga1_3	RSP-6 overexpression	raga-1

Showing results 1 to 12 of 12

Showing results 1 to 12 of 12

Collection:

Collection ID:	CO003443
Collection Summary:	Animals were collected and washed 3 times with M9 buffer and once quickly with HPLC-grade water quickly and flash-frozen in liquid nitrogen. Metabolites were extracted using 800µL of 40:40:20 acetonitrile:methanol:water solvent at -20ºC, vortexed for 10 sec, and further lysed with a TissueLyser LT (Qiagen) with stainless steel beads.
Sample Type:	Worms

Treatment:

Treatment ID:	TR003459
Treatment Summary:	All worms were passaged on NGM with OP50 bacteria for at least two generations before the assay. For metabolomics, 25,000 second generation L1 animals treated with RNAi against EV or raga-1 were incubated on NGM with the corresponding food source for 4 hours.

Sample Preparation:

Sampleprep ID:	SP003457
Sampleprep Summary:	Metabolites were resolved on a Vanquish U-HPLC system coupled to a Q Exactive HF-X hybrid quadrupole-orbitrap mass spectrometer (ThermoFisher) with a HESI source operating in negative ion mode. The analytes were separated by using an iHILIC column (5μm, 150 × 2.1 mm I.D., HILICON) coupled to a Thermo Scientific SII UPLC system. The iHILIC column was used with the following buffers and linear gradient: Buffer A = water with 20 mM ammonium carbonate with 0.1% ammonium hydroxide, Buffer B = 100% acetonitrile. The gradient was run at a flow rate of 0.150 mL/min as follows: 0-23min linear gradient from 95% B to 5% B; 23-25min hold at 5%B. To waste from 25-25.5min gradient to 95% B at 0.20 mL/min, 25.5-32.5min hold at 95%B and finally 32.5-33min 95%B at 0.15 mL/min. MS data acquisition and targeted feature extraction and quantification were performed using TraceFinder 5.1 or open-source EL-MAVEN software. Peak area integration and metabolite identification were done using accurate mass and retention time curated with in-house standard library compounds. Three biological replicates were used for each condition.

Sampleprep ID:

SP003457

Sampleprep Summary:

Metabolites were resolved on a Vanquish U-HPLC system coupled to a Q Exactive HF-X hybrid quadrupole-orbitrap mass spectrometer (ThermoFisher) with a HESI source operating in negative ion mode. The analytes were separated by using an iHILIC column (5μm, 150 × 2.1 mm I.D., HILICON) coupled to a Thermo Scientific SII UPLC system. The iHILIC column was used with the following buffers and linear gradient: Buffer A = water with 20 mM ammonium carbonate with 0.1% ammonium hydroxide, Buffer B = 100% acetonitrile. The gradient was run at a flow rate of 0.150 mL/min as follows: 0-23min linear gradient from 95% B to 5% B; 23-25min hold at 5%B. To waste from 25-25.5min gradient to 95% B at 0.20 mL/min, 25.5-32.5min hold at 95%B and finally 32.5-33min 95%B at 0.15 mL/min. MS data acquisition and targeted feature extraction and quantification were performed using TraceFinder 5.1 or open-source EL-MAVEN software. Peak area integration and metabolite identification were done using accurate mass and retention time curated with in-house standard library compounds. Three biological replicates were used for each condition.

Chromatography:

Chromatography ID:	CH004141
Instrument Name:	Thermo Vanquish
Column Name:	iHILIC®-(P) Classic HILIC Column PEEK (150 x 2.1mm, 5µm) Cat.# W 160.152.0520
Column Temperature:	30ºC
Flow Gradient:	0-23 min linear gradient from 95% B to 5% B; 23-25 min hold at 5% B
Flow Rate:	0.150 mL/min
Solvent A:	100% Water; 20 mM ammonium carbonate, 0.1% ammonium hydroxide
Solvent B:	100% Acetonitrile
Chromatography Type:	HILIC

Analysis:

Analysis ID:	AN005454
Analysis Type:	MS
Chromatography ID:	CH004141
Num Factors:	4
Num Metabolites:	96
Units:	pmoles/L