Summary of Study ST002184

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 PR001391. The data can be accessed directly via it's Project DOI: 10.21228/M8X99S This work is supported by NIH grant, U2C- DK119886.

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Study IDST002184
Study TitleMetabolic effect of the loss of mitochondrial-specific aspartyl-tRNA synthetase Das2 on mouse intestinal epithelial cells
Study SummaryWe analysed the intestinal epithelial cell (IEC) from Dars2 fl/fl ; VillinCreERT2 tg/wt mice (n=15) and and Dars2 fl/fl ; VillinCreERT2 wt/wt mice (n=9) at 8 days upon tamoxifen injection to assess the metabolic effect of Das2 loss. Isolated IECs were divided into three technical replicates (n=69) and analysed with two analytical repeats (n=138).
Institute
CECAD Research Center
Last NameYang
First NameMing
AddressJoseph-Stelzmann-Straße 26, Köln, Koeln, 50931, Germany
Emailming.yang@uni-koeln.de
Phone4922147884306
Submit Date2022-06-01
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-06-15
Release Version1
Ming Yang Ming Yang
https://dx.doi.org/10.21228/M8X99S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001391
Project DOI:doi: 10.21228/M8X99S
Project Title:Mitochondria regulate dietary lipid processing in enterocytes
Project Summary:Digested dietary fats are taken up, processed and transported by enterocytes to supply the body with lipids. Most absorbed lipids are assembled into pre-chylomicrons in the endoplasmic reticulum (ER) of enterocytes, which are then transported to the Golgi for maturation and subsequent secretion to the circulation. The role of mitochondria in regulating intestinal lipid transport remains unknown. Here we show that mitochondrial dysfunction in enterocytes inhibits chylomicron production and the transport of dietary lipids to peripheral organs. Mice with intestinal epithelial cell (IEC)-specific ablation of the mitochondrial-specific aspartyl - tRNA synthetase DARS2, as well as of the respiratory chain subunit SDHA or the assembly factor COX10 failed to thrive and showed massive accumulation of lipids within large lipid droplets (LDs) in enterocytes of the proximal small intestine (SI). Feeding a fat-free diet inhibited the formation of LDs in DARS2-deficient enterocytes, showing that accumulating lipids derive mostly from digested fat. Furthermore, metabolic tracing studies revealed impaired transport of dietary lipids to peripheral organs in mice lacking DARS2 in IECs. Moreover, DARS2-deficient enterocytes showed a distinct lack of mature chylomicrons concomitant with a disorganisation of the Golgi apparatus, suggesting that impaired ER to Golgi trafficking underlies impaired chylomicron production and secretion. Taken together, these results revealed a vital role of mitochondria in regulating dietary lipid transport in enterocytes, which is relevant for understanding the intestinal and nutritional defects observed in patients with mitochondrial defects.
Institute:CECAD Research Center
Last Name:Yang
First Name:Ming
Address:Joseph-Stelzmann-Straße 26, Köln, Koeln, 50931, Germany
Email:ming.yang@uni-koeln.de
Phone:4922147884306

Subject:

Subject ID:SU002270
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Genotype Tissue type
SA209872CM02b-015Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209873CM02b-016Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209874CM02b-014Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209875CM02b-013Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209876CM02b-009Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209877CM02b-017Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209878CM02b-019Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209879CM02b-022Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209880CM02b-023Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209881CM02b-021Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209882CM02b-020Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209883CM02b-008Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209884CM02b-018Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209885CM02b-006Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209886CM02-064Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209887CM02-065Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209888CM02-063Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209889CM02-062Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209890CM02-061Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209891CM02-066Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209892CM02-070Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209893CM02b-005Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209894CM02b-024Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209895CM02-004Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209896CM02-072Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209897CM02-071Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209898CM02b-007Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209899CM02b-029Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209900CM02b-061Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209901CM02b-062Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209902CM02b-060Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209903CM02b-059Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209904CM02b-058Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209905CM02b-063Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209906CM02b-064Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209907CM02b-071Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209908CM02b-072Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209909CM02b-070Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209910CM02b-066Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209911CM02b-065Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209912CM02b-057Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209913CM02b-056Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209914CM02b-044Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209915CM02b-045Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209916CM02b-043Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209917CM02b-030Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209918CM02-060Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209919CM02b-046Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209920CM02b-047Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209921CM02b-054Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209922CM02b-055Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209923CM02b-053Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209924CM02b-052Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209925CM02b-048Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209926CM02b-028Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209927CM02b-004Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209928CM02-015Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209929CM02-016Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209930CM02-017Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209931CM02-014Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209932CM02-013Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209933CM02-044Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209934CM02-043Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209935CM02-018Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209936CM02-019Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209937CM02-024Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209938CM02-059Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209939CM02-030Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209940CM02-023Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209941CM02-022Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209942CM02-020Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209943CM02-021Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209944CM02-028Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209945CM02-009Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209946CM02-005Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209947CM02-006Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209948CM02-007Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209949CM02-053Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209950CM02-054Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209951CM02-055Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209952CM02-058Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209953CM02-057Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209954CM02-056Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209955CM02-052Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209956CM02-008Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209957CM02-045Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209958CM02-047Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209959CM02-046Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209960CM02-048Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209961CM02-029Das2_VillinCreERT2_tg/wt intestinal epithelial cells
SA209962CM02b-049Das2_VillinCreERT2_wt/wt intestinal epithelial cells
SA209963CM02-027Das2_VillinCreERT2_wt/wt intestinal epithelial cells
SA209964CM02-025Das2_VillinCreERT2_wt/wt intestinal epithelial cells
SA209965CM02b-042Das2_VillinCreERT2_wt/wt intestinal epithelial cells
SA209966CM02-026Das2_VillinCreERT2_wt/wt intestinal epithelial cells
SA209967CM02-011Das2_VillinCreERT2_wt/wt intestinal epithelial cells
SA209968CM02b-067Das2_VillinCreERT2_wt/wt intestinal epithelial cells
SA209969CM02b-068Das2_VillinCreERT2_wt/wt intestinal epithelial cells
SA209970CM02b-069Das2_VillinCreERT2_wt/wt intestinal epithelial cells
SA209971CM02-010Das2_VillinCreERT2_wt/wt intestinal epithelial cells
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Collection:

Collection ID:CO002263
Collection Summary:Small intestines were dissected and washed with PBS. Small pieces of approximately ~0.5 cm were isolated from proximal (post stomach) small intestine and snap frozen on dry ice and stored at -80°C until further processing. The remaining small intestinal tissue was washed in PBS to remove faeces and cut longitudinally. Intestinal epithelial cells were isolated by sequential incubation of intestinal tissue in pre-heated 1 mM dithiothreitol and 1.5 mM EDTA solutions at 37oC while shaking. Intestinal epithelial cell pellet was frozen at -80°C until further processing. Intestinal epithelial cell (IEC) pellet was frozen at -80oC for further processing.
Sample Type:Intestine

Treatment:

Treatment ID:TR002282
Treatment Summary:VillinCreERT2 recombinase activity was induced by five consecutive daily intraperitoneal administrations of 1 mg tamoxifen dissolved in corn oil/DMSO. Small intestine tissue and intestinal epithelial cells were harvested 8 days post last tamoxifen treatment.

Sample Preparation:

Sampleprep ID:SP002276
Sampleprep Summary:Metabolite extraction solution (50% methanol, 30% acetonitrile, 20% water, 5uM valine-d8 as internal standard) was added to (10-20mg) frozen small intestine tissue samples at an extraction ratio of 25ul/mg on dry ice. Samples were then homogenized using a Precellys 24 tissue homogenizer (Bertin technologies). The resulting sample suspension was vortexed, mixed at 4oC in a Thermomixer for 15 min at 1,500 rpm and then centrifuged at 16,000 x g for 20 min at 4oC. The supernatant was collected for LC-MS analysis.

Combined analysis:

Analysis ID AN003577
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Dionex Ultimate 3000
Column SeQuant ZIC- pHILIC (150 x 2.1mm, 5um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units peak area

Chromatography:

Chromatography ID:CH002645
Chromatography Summary:LC-MS chromatographic separation of metabolites was achieved using a Millipore Sequant ZIC-pHILIC analytical column (5 µm, 2.1 × 150 mm) equipped with a 2.1 × 20 mm guard column (both 5 mm particle size) with a binary solvent system. Solvent A was 20 mM ammonium carbonate, 0.05% ammonium hydroxide; Solvent B was acetonitrile. The column oven and autosampler tray were held at 40°C and 4 °C, respectively. The chromatographic gradient was run at a flow rate of 0.200 mL/min as follows: 0–2 min: 80% B; 2-17 min: linear gradient from 80% B to 20% B; 17-17.1 min: linear gradient from 20% B to 80% B; 17.1-22.5 min: hold at 80% B. Samples were randomized and analysed with LC–MS in a blinded manner with an injection volume of 5 µl. Pooled samples were generated from an equal mixture of all individual samples and analysed interspersed at regular intervals within sample sequence as a quality control.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:SeQuant ZIC- pHILIC (150 x 2.1mm, 5um)
Chromatography Type:HILIC

MS:

MS ID:MS003334
Analysis ID:AN003577
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolites were measured with a Thermo Scientific Q Exactive Hybrid Quadrupole-Orbitrap Mass spectrometer (HRMS) coupled to a Dionex Ultimate 3000 UHPLC. The mass spectrometer was operated in full-scan, polarity-switching mode, with the spray voltage set to +4.5 kV/-3.5 kV, ion transfer tube temperature set to 320 °C, the vaporizer temperature set to 280 °C, the sheath gas flow set to 55 units, the auxiliary gas flow set to 15 units, and the sweep gas flow set to 0 unit. HRMS data acquisition was performed in a range of m/z = 70–900, with the resolution set at 70,000, the AGC target at 1 × 106, and the maximum injection time (Max IT) at 120 ms. Chromatogram review and peak area integration were performed using the Thermo Fisher software Tracefinder (v.5.0). Metabolite identities were confirmed using two parameters: (1) precursor ion m/z was matched within 5 ppm of theoretical mass predicted by the chemical formula; (2) the retention time of metabolites was within 5% of the retention time of a purified standard run with the same chromatographic method.
Ion Mode:UNSPECIFIED
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