Summary of Study ST002125

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.

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	ST002125
Study Title	Amino acids and TCA substrates in hematopoietic cells (Part2)
Study Summary	This 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 Name	Zhao
First Name	Meng
Address	Zhongshan 2nd Road
Email	zhaom38@mail.sysu.edu.cn
Phone	18138799889
Submit Date	2022-04-06
Raw Data Available	Yes
Raw Data File Type(s)	cdf
Analysis Type Detail	GC-MS
Release Date	2022-11-01
Release Version	1

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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:	SU002210
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
SA204320	BM_supernatant_5FU_1	Bone marrow supernatant	5 FU 2 weeks	1c	Unlabeled AAs were used for total AA (FigS2.D)
SA204321	BM_supernatant_5FU_2	Bone marrow supernatant	5 FU 2 weeks	1c	Unlabeled AAs were used for total AA (FigS2.D)
SA204322	BM_supernatant_5FU_3	Bone marrow supernatant	5 FU 2 weeks	1c	Unlabeled AAs were used for total AA (FigS2.D)
SA204323	BM_supernatant_Ctrl_1	Bone marrow supernatant	HSC Basal	1c	Unlabeled AAs were used for total AA (FigS2.D)
SA204324	BM_supernatant_Ctrl_2	Bone marrow supernatant	HSC Basal	1c	Unlabeled AAs were used for total AA (FigS2.D)
SA204325	BM_supernatant_Ctrl_3	Bone marrow supernatant	HSC Basal	1c	Unlabeled AAs were used for total AA (FigS2.D)
SA204326	HSC_5FU_1	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	5 FU 2 weeks, [13C, 15N] AAs were incorporated for 1 h	1c	[13C, 15N] AAs were used for AA uptake (Fig2.B, Fig5M); unlabeled AAs and TCA substrate were used for total AA levels (Fig2.C, Fig5K) and TCA substrate levels (Fig2.K, Fig5J).
SA204327	HSC_5FU_3	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	5 FU 2 weeks, [13C, 15N] AAs were incorporated for 1 h	1c	[13C, 15N] AAs were used for AA uptake (Fig2.B, Fig5M); unlabeled AAs and TCA substrate were used for total AA levels (Fig2.C, Fig5K) and TCA substrate levels (Fig2.K, Fig5J).
SA204328	HSC_5FU_2	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	5 FU 2 weeks, [13C, 15N] AAs were incorporated for 1 h	1c	[13C, 15N] AAs were used for AA uptake (Fig2.B, Fig5M); unlabeled AAs and TCA substrate were used for total AA levels (Fig2.C, Fig5K) and TCA substrate levels (Fig2.K, Fig5J).
SA204329	HSC_5FU_0h_3	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	5 FU 2 weeks, [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 (Fig2.D).
SA204330	HSC_5FU_0h_2	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	5 FU 2 weeks, [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 (Fig2.D).
SA204331	HSC_5FU_0h_1	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	5 FU 2 weeks, [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 (Fig2.D).
SA204332	HSC_5FU_12h_3	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	5 FU 2 weeks, [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 (Fig2.D).
SA204333	HSC_5FU_12h_1	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	5 FU 2 weeks, [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 (Fig2.D).
SA204334	HSC_5FU_12h_2	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	5 FU 2 weeks, [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 (Fig2.D).
SA204335	HSC_5FU_6h_1	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	5 FU 2 weeks, [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 (Fig2.D).
SA204336	HSC_5FU_6h_3	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	5 FU 2 weeks, [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 (Fig2.D).
SA204337	HSC_5FU_6h_2	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	5 FU 2 weeks, [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 (Fig2.D).
SA204338	HSC_Cultured_3	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	Ex vivo culture 2 weeks, [13C, 15N] AAs were incorporated for 1 h	1c	[13C, 15N] AAs were used for AA uptake (Fig2.B); unlabeled AAs and TCA substrate were used for total AA levels (Fig2.C) and TCA substrate levels (Fig2.K).
SA204339	HSC_Cultured_2	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	Ex vivo culture 2 weeks, [13C, 15N] AAs were incorporated for 1 h	1c	[13C, 15N] AAs were used for AA uptake (Fig2.B); unlabeled AAs and TCA substrate were used for total AA levels (Fig2.C) and TCA substrate levels (Fig2.K).
SA204340	HSC_Cultured_1	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	Ex vivo culture 2 weeks, [13C, 15N] AAs were incorporated for 1 h	1c	[13C, 15N] AAs were used for AA uptake (Fig2.B); unlabeled AAs and TCA substrate were used for total AA levels (Fig2.C) and TCA substrate levels (Fig2.K).
SA204341	HSC_Cultured_6h_1	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	Ex vivo culture 2 weeks, [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 (Fig2.D).
SA204342	HSC_Cultured_0h_1	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	Ex vivo culture 2 weeks, [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 (Fig2.D).
SA204343	HSC_Cultured_0h_2	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	Ex vivo culture 2 weeks, [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 (Fig2.D).
SA204344	HSC_Cultured_0h_3	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	Ex vivo culture 2 weeks, [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 (Fig2.D).
SA204345	HSC_Cultured_12h_3	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	Ex vivo culture 2 weeks, [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 (Fig2.D).
SA204346	HSC_Cultured_12h_2	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	Ex vivo culture 2 weeks, [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 (Fig2.D).
SA204347	HSC_Cultured_12h_1	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	Ex vivo culture 2 weeks, [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 (Fig2.D).
SA204348	HSC_Cultured_6h_2	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	Ex vivo culture 2 weeks, [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 (Fig2.D).
SA204349	HSC_Cultured_6h_3	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	Ex vivo culture 2 weeks, [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 (Fig2.D).
SA204353	HSC_Ctrl_0h_2	Lin– 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).
SA204354	HSC_Ctrl_0h_3	Lin– 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).
SA204355	HSC_Ctrl_0h_1	Lin– 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).
SA204356	HSC_Ctrl_12h_3	Lin– 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).
SA204357	HSC_Ctrl_12h_2	Lin– 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).
SA204358	HSC_Ctrl_12h_1	Lin– 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).
SA204359	HSC_Ctrl_6h_1	Lin– 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).
SA204360	HSC_Ctrl_6h_2	Lin– 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).
SA204361	HSC_Ctrl_6h_3	Lin– 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).
SA204350	HSC_Ctrl_3	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	HSC Basal or Ctrl, [13C, 15N] AAs were incorporated for 1 h	1c	[13C, 15N] AAs were used for AA uptake (Fig2.B, Fig5M); unlabeled AAs and TCA substrate were used for total AA levels (Fig2.C, Fig5K) and TCA substrate levels (Fig2.K, Fig5J).
SA204351	HSC_Ctrl_1	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	HSC Basal or Ctrl, [13C, 15N] AAs were incorporated for 1 h	1c	[13C, 15N] AAs were used for AA uptake (Fig2.B, Fig5M); unlabeled AAs and TCA substrate were used for total AA levels (Fig2.C, Fig5K) and TCA substrate levels (Fig2.K, Fig5J).
SA204352	HSC_Ctrl_2	Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC)	HSC Basal or Ctrl, [13C, 15N] AAs were incorporated for 1 h	1c	[13C, 15N] AAs were used for AA uptake (Fig2.B, Fig5M); unlabeled AAs and TCA substrate were used for total AA levels (Fig2.C, Fig5K) and TCA substrate levels (Fig2.K, Fig5J).

Showing results 1 to 42 of 42

Showing results 1 to 42 of 42

Collection:

Collection ID:	CO002203
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:	TR002222
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:	SP002216
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).

Sampleprep ID:

SP002216

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	AN003478
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:	CH002567
Instrument Name:	TRACE 1310
Column Name:	DB-35ms
Chromatography Type:	GC

MS:

MS ID:	MS003239
Analysis ID:	AN003478
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