Summary of Study ST002124

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 PR001348. The data can be accessed directly via it's Project DOI: 10.21228/M8GD8D This work is supported by NIH grant, U2C- DK119886.

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Study IDST002124
Study TitleAmino acids and TCA substrates in hematopoietic cells (Part1)
Study SummaryThis study uses [13C,15N] labeled amino acids to study the amino acid consumption and their catabolism into tricarboxylic acid cycle substrates in hematopoietic stem cells, hemopoietic progenitors, and differentiated hematopoietic cells under different conditions, such as homeostasis and proliferation and with drug treatment.
Institute
Sun Yat-sen University
Last NameZhao
First NameMeng
AddressZhongshan 2nd Road
Emailzhaom38@mail.sysu.edu.cn
Phone18138799889
Submit Date2022-04-06
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2022-11-01
Release Version1
Meng Zhao Meng Zhao
https://dx.doi.org/10.21228/M8GD8D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001348
Project DOI:doi: 10.21228/M8GD8D
Project Title:Amino acid catabolism in hematopoietic cells
Project Summary:Hematopoietic stem cells (HSCs) adapt their metabolism to maintenance and proliferation, but the mechanism remains incompletely understood. Here, we have investigated the total levels, uptake and catabolism of amino acid in hematopoietic stem cells, hemopoietic progenitors, and differentiated hematopoietic cells. We have also studied the catabolism of amino acid in hematopoietic stem cells under different conditions, such as homeostasis and proliferation and with drug treatment. Moreover, glycolytic metabolite, NAD+ precursor nicotinamide riboside (NR), accelerated AA catabolism to activate GCN2 and sustain long-term function of HSCs. Overall, our study uncovers the direct links between metabolic alterations and translation control in HSCs during homeostasis and proliferation.
Institute:Sun Yat-sen University
Last Name:Zhao
First Name:Meng
Address:Zhongshan 2nd Road
Email:zhaom38@mail.sysu.edu.cn
Phone:18138799889

Subject:

Subject ID:SU002209
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 Source_Name[gating] Treatment Batch Note
SA204272Lin–_2Lineage-negative (Lin–) [13C, 15N] AAs were incorporated for 1 h 1a [13C, 15N] AAs were used for AA uptake (Fig1.B); unlabeled AAs were used for total AA (Fig1.A) and TCA substrate levels (Fig1.D).
SA204273Lin–_1Lineage-negative (Lin–) [13C, 15N] AAs were incorporated for 1 h 1a [13C, 15N] AAs were used for AA uptake (Fig1.B); unlabeled AAs were used for total AA (Fig1.A) and TCA substrate levels (Fig1.D).
SA204274Lin–_3Lineage-negative (Lin–) [13C, 15N] AAs were incorporated for 1 h 1a [13C, 15N] AAs were used for AA uptake (Fig1.B); unlabeled AAs were used for total AA (Fig1.A) and TCA substrate levels (Fig1.D).
SA204275Lin–_0h_2Lineage-negative (Lin–) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 0 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204276Lin–_0h_1Lineage-negative (Lin–) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 0 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204277Lin–_0h_3Lineage-negative (Lin–) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 0 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204278Lin–_12h_1Lineage-negative (Lin–) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 12 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204279Lin–_12h_2Lineage-negative (Lin–) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 12 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204280Lin–_12h_3Lineage-negative (Lin–) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 12 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204281Lin–_6h_2Lineage-negative (Lin–) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 6 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204282Lin–_6h_3Lineage-negative (Lin–) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 6 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204283Lin–_6h_1Lineage-negative (Lin–) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 6 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204305HSC_1Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC) [13C, 15N] AAs were incorporated for 1 h 1a [13C, 15N] AAs were used for AA uptake (Fig1.B); unlabeled AAs were used for total AA (Fig1.A) and TCA substrate levels (Fig1.D).
SA204306HSC_3Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC) [13C, 15N] AAs were incorporated for 1 h 1a [13C, 15N] AAs were used for AA uptake (Fig1.B); unlabeled AAs were used for total AA (Fig1.A) and TCA substrate levels (Fig1.D).
SA204307HSC_2Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC) [13C, 15N] AAs were incorporated for 1 h 1a [13C, 15N] AAs were used for AA uptake (Fig1.B); unlabeled AAs were used for total AA (Fig1.A) and TCA substrate levels (Fig1.D).
SA204296HSC_Ctrl_0h_3Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC) HSC Basal, [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 0 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C, Fig2.D).
SA204297HSC_Ctrl_0h_2Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC) HSC Basal, [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 0 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C, Fig2.D).
SA204298HSC_Ctrl_0h_1Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC) HSC Basal, [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 0 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C, Fig2.D).
SA204299HSC_Ctrl_12h_2Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC) HSC Basal, [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 12 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C, Fig2.D).
SA204300HSC_Ctrl_12h_3Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC) HSC Basal, [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 12 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C, Fig2.D).
SA204301HSC_Ctrl_12h_1Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC) HSC Basal, [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 12 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C, Fig2.D).
SA204302HSC_Ctrl_6h_3Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC) HSC Basal, [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 6 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C, Fig2.D).
SA204303HSC_Ctrl_6h_1Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC) HSC Basal, [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 6 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C, Fig2.D).
SA204304HSC_Ctrl_6h_2Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC) HSC Basal, [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 6 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C, Fig2.D).
SA204284LSK_3Lin– Scal1+ c-Kit+ (LSK) [13C, 15N] AAs were incorporated for 1 h 1a [13C, 15N] AAs were used for AA uptake (Fig1.B); unlabeled AAs were used for total AA (Fig1.A) and TCA substrate levels (Fig1.D).
SA204285LSK_2Lin– Scal1+ c-Kit+ (LSK) [13C, 15N] AAs were incorporated for 1 h 1a [13C, 15N] AAs were used for AA uptake (Fig1.B); unlabeled AAs were used for total AA (Fig1.A) and TCA substrate levels (Fig1.D).
SA204286LSK_1Lin– Scal1+ c-Kit+ (LSK) [13C, 15N] AAs were incorporated for 1 h 1a [13C, 15N] AAs were used for AA uptake (Fig1.B); unlabeled AAs were used for total AA (Fig1.A) and TCA substrate levels (Fig1.D).
SA204287LSK_0h_2Lin– Scal1+ c-Kit+ (LSK) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 0 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204288LSK_0h_3Lin– Scal1+ c-Kit+ (LSK) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 0 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204289LSK_0h_1Lin– Scal1+ c-Kit+ (LSK) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 0 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204290LSK_12h_1Lin– Scal1+ c-Kit+ (LSK) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 12 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204291LSK_12h_2Lin– Scal1+ c-Kit+ (LSK) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 12 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204292LSK_12h_3Lin– Scal1+ c-Kit+ (LSK) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 12 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204293LSK_6h_3Lin– Scal1+ c-Kit+ (LSK) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 6 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204294LSK_6h_2Lin– Scal1+ c-Kit+ (LSK) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 6 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204295LSK_6h_1Lin– Scal1+ c-Kit+ (LSK) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 6 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204308Lin+_3Mature hematopoietic cells (Lin+ cells) [13C, 15N] AAs were incorporated for 1 h 1a [13C, 15N] AAs were used for AA uptake (Fig1.B); unlabeled AAs were used for total AA (Fig1.A) and TCA substrate levels (Fig1.D).
SA204309Lin+_1Mature hematopoietic cells (Lin+ cells) [13C, 15N] AAs were incorporated for 1 h 1a [13C, 15N] AAs were used for AA uptake (Fig1.B); unlabeled AAs were used for total AA (Fig1.A) and TCA substrate levels (Fig1.D).
SA204310Lin+_2Mature hematopoietic cells (Lin+ cells) [13C, 15N] AAs were incorporated for 1 h 1a [13C, 15N] AAs were used for AA uptake (Fig1.B); unlabeled AAs were used for total AA (Fig1.A) and TCA substrate levels (Fig1.D).
SA204311Lin+_0h_1Mature hematopoietic cells (Lin+ cells) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 0 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204312Lin+_0h_3Mature hematopoietic cells (Lin+ cells) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 0 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204313Lin+_0h_2Mature hematopoietic cells (Lin+ cells) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 0 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204314Lin+_12h_2Mature hematopoietic cells (Lin+ cells) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 12 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204315Lin+_12h_3Mature hematopoietic cells (Lin+ cells) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 12 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204316Lin+_12h_1Mature hematopoietic cells (Lin+ cells) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 12 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204317Lin+_6h_1Mature hematopoietic cells (Lin+ cells) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 6 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204318Lin+_6h_2Mature hematopoietic cells (Lin+ cells) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 6 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
SA204319Lin+_6h_3Mature hematopoietic cells (Lin+ cells) [13C, 15N] AAs were incorporated for 24 h and subsequently washed out for 6 h 1b [13C, 15N] AA levels and [13C]TCA substrate levels in different time point were calculated for AA catabolism (Fig1.C).
Showing results 1 to 48 of 48

Collection:

Collection ID:CO002202
Collection Summary:5×10^5 indicated cells were incubated with 100 µM stable [13C,15N] amino acids (MSK-A2-US-1.2, Cambridge Isotope Laboratories) for indicated time and centrifuged at 500 g for 5 min at 4 °C. The pelleted cells were extracted in 500 µl ice-cold Acetonitrile: Isopropyl Alcohol: water (3:3:2 v/v/v) and aliquoted as three technical replicates. The extracts were vortexed for 5 min at 4 °C and centrifuged at 14,000 g for 2 min at 4 °C. The supernatants were dried by vacuum spin for subsequent derivatization and stored at -20 ℃.
Sample Type:Bone marrow

Treatment:

Treatment ID:TR002221
Treatment Summary:Germ-free C57BL/6J mice were intraperitoneally injected with 10 mg/kg 5FU (F6627-5G, Sigma-Aldrich) for 14 days, or fed with vehicle or NR (400 mg/kg per day) (1341-23-7, ziyi-reagent) for consecutive 8 weeks (long-term) or 1 week (short-term). Hematopoietic cells were stained and sorted from treated mice.

Sample Preparation:

Sampleprep ID:SP002215
Sampleprep Summary:To get the corresponding derivatives, the dried aliquots were incubated with 20 µL 2% (w/v) methoxyamine hydrochloride (226904, Sigma-Aldrich) in pyridine for 60 min at 37 °C, and silylated by 30 µL of N-Methyl-N-(tert-butyldimethylsilyl) trifluoroacetamide with 1% tert-Butyldimethylchlorosilane (TBDMS, 18162-48-6, Regis Technologies) for 30 min at 45 °C. The corresponding derivatives were analyzed by GC-MS using the Trace 1310 gas chromatograph (Thermo Fisher) with the DB-35ms column (Agilent Technologies) connected to the Q ExactiveTM GC OrbitrapTM GC-MS/MS system (Thermo Fisher).

Combined analysis:

Analysis ID AN003477
Analysis type MS
Chromatography type GC
Chromatography system TRACE 1310
Column DB-35ms
MS Type EI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode POSITIVE
Units Peak Area

Chromatography:

Chromatography ID:CH002566
Instrument Name:TRACE 1310
Column Name:DB-35ms
Chromatography Type:GC

MS:

MS ID:MS003238
Analysis ID:AN003477
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:EI
MS Comments:GC-MS data was acquired on Q-Exactive Orbitrap mass spectrometer (Thermo Fisher) coupled with Gas Chromatograph system TRACE 1310 (Thermo Fisher). Chromatographic separation was performed on a DB-35ms column module (30 m length x 0.25 mm internal diameter, Agilent Technologies). The column temperature was programmed with an initial temperature of 50 °C for 2 min, then ramped at 10°C/min to 325 °C, and maintained for 5 min. The mass range was set as 50-600 m/z, and the resolution was 60,000. The ion source temperature was 300°C with the transfer line temperature of 250°C, and the electron energy was 70 eV with EI source.
Ion Mode:POSITIVE
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