Summary of Study ST003001

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 PR001871. The data can be accessed directly via it's Project DOI: 10.21228/M8VX4G 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.

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Study ID	ST003001
Study Title	The Track Dairy Cattle (trackDC) study
Study Summary	The Track Dairy Cattle (trackDC) study is a longitudinal study in northern China that aims to track newborn calves to assess the development of gut microbiota during early life that contributes to cattle health and production. In this study, 36 newborn calves were randomly assigned to three groups and followed for two months after birth. The groups included a control group (CON), a rumen microbiota transplantation group (RMT), and a rumen fluid transplantation group (RFT) and intensive data has been collected. Blood samples were collected at 15, 35, and 56 days after birth.
Institute	Nanjing Medical University
Last Name	Dong
First Name	Quanbin
Address	No. 215 Guangzhou road
Email	qbdong@stu.njmu.edu.cn
Phone	15311095435
Submit Date	2023-12-10
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2023-12-12
Release Version	1

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Project:

Project ID:	PR001871
Project DOI:	doi: 10.21228/M8VX4G
Project Title:	The Track Dairy Cattle (trackDC) study
Project Summary:	The Track Dairy Cattle (trackDC) study is a longitudinal study in northern China that aims to track newborn calves to assess the development of gut microbiota during early life that contributes to cattle health and production. In this study, 36 newborn calves were randomly assigned to three groups and followed for two months after birth. The groups included a control group (CON), a rumen microbiota transplantation group (RMT), and a rumen fluid transplantation group (RFT) and intensive data has been collected. Blood samples were collected at 15, 35, and 56 days after birth.
Institute:	Nanjing Medical University
Last Name:	Dong
First Name:	Quanbin
Address:	No. 215 Guangzhou road
Email:	qbdong@stu.njmu.edu.cn
Phone:	15311095435

Subject:

Subject ID:	SU003114
Subject Type:	Mammal
Subject Species:	Bos taurus
Taxonomy ID:	9913

Factors:

Subject type: Mammal; Subject species: Bos taurus (Factor headings shown in green)

mb_sample_id	local_sample_id	Transplantation group
SA326558	F86_0	CON \| collection_timepoint:0
SA326559	F84_0	CON \| collection_timepoint:0
SA326560	F64_0	CON \| collection_timepoint:0
SA326561	F87_0	CON \| collection_timepoint:0
SA326562	F65_0	CON \| collection_timepoint:0
SA326563	F89_0	CON \| collection_timepoint:0
SA326564	F92_0	CON \| collection_timepoint:0
SA326565	F91_0	CON \| collection_timepoint:0
SA326566	F90_0	CON \| collection_timepoint:0
SA326567	F63_0	CON \| collection_timepoint:0
SA326568	F88_0	CON \| collection_timepoint:0
SA326569	F62_0	CON \| collection_timepoint:0
SA326570	F65_15	CON \| collection_timepoint:15
SA326571	F63_15	CON \| collection_timepoint:15
SA326572	F62_15	CON \| collection_timepoint:15
SA326573	F92_15	CON \| collection_timepoint:15
SA326574	F84_15	CON \| collection_timepoint:15
SA326575	F64_15	CON \| collection_timepoint:15
SA326576	F88_15	CON \| collection_timepoint:15
SA326577	F91_15	CON \| collection_timepoint:15
SA326578	F87_15	CON \| collection_timepoint:15
SA326579	F89_15	CON \| collection_timepoint:15
SA326580	F86_15	CON \| collection_timepoint:15
SA326581	F90_15	CON \| collection_timepoint:15
SA326582	F84_35	CON \| collection_timepoint:35
SA326583	F92_35	CON \| collection_timepoint:35
SA326584	F62_35	CON \| collection_timepoint:35
SA326585	F91_35	CON \| collection_timepoint:35
SA326586	F63_35	CON \| collection_timepoint:35
SA326587	F64_35	CON \| collection_timepoint:35
SA326588	F65_35	CON \| collection_timepoint:35
SA326589	F87_35	CON \| collection_timepoint:35
SA326590	F90_35	CON \| collection_timepoint:35
SA326591	F88_35	CON \| collection_timepoint:35
SA326592	F86_35	CON \| collection_timepoint:35
SA326593	F89_35	CON \| collection_timepoint:35
SA326594	F90_56	CON \| collection_timepoint:56
SA326595	F89_56	CON \| collection_timepoint:56
SA326596	F64_56	CON \| collection_timepoint:56
SA326597	F92_56	CON \| collection_timepoint:56
SA326598	F88_56	CON \| collection_timepoint:56
SA326599	F91_56	CON \| collection_timepoint:56
SA326600	F87_56	CON \| collection_timepoint:56
SA326601	F63_56	CON \| collection_timepoint:56
SA326602	F62_56	CON \| collection_timepoint:56
SA326603	F84_56	CON \| collection_timepoint:56
SA326604	F86_56	CON \| collection_timepoint:56
SA326605	F65_56	CON \| collection_timepoint:56
SA326606	F67_0	RFT \| collection_timepoint:0
SA326607	F66_0	RFT \| collection_timepoint:0
SA326608	F69_0	RFT \| collection_timepoint:0
SA326609	F68_0	RFT \| collection_timepoint:0
SA326610	F77_0	RFT \| collection_timepoint:0
SA326611	F80_0	RFT \| collection_timepoint:0
SA326612	F83_0	RFT \| collection_timepoint:0
SA326613	F79_0	RFT \| collection_timepoint:0
SA326614	F76_0	RFT \| collection_timepoint:0
SA326615	F73_0	RFT \| collection_timepoint:0
SA326616	F75_0	RFT \| collection_timepoint:0
SA326617	F70_0	RFT \| collection_timepoint:0
SA326618	F79_15	RFT \| collection_timepoint:15
SA326619	F69_15	RFT \| collection_timepoint:15
SA326620	F68_15	RFT \| collection_timepoint:15
SA326621	F66_15	RFT \| collection_timepoint:15
SA326622	F83_15	RFT \| collection_timepoint:15
SA326623	F70_15	RFT \| collection_timepoint:15
SA326624	F67_15	RFT \| collection_timepoint:15
SA326625	F77_15	RFT \| collection_timepoint:15
SA326626	F76_15	RFT \| collection_timepoint:15
SA326627	F80_15	RFT \| collection_timepoint:15
SA326628	F73_15	RFT \| collection_timepoint:15
SA326629	F75_15	RFT \| collection_timepoint:15
SA326630	F70_35	RFT \| collection_timepoint:35
SA326631	F68_35	RFT \| collection_timepoint:35
SA326632	F67_35	RFT \| collection_timepoint:35
SA326633	F75_35	RFT \| collection_timepoint:35
SA326634	F69_35	RFT \| collection_timepoint:35
SA326635	F79_35	RFT \| collection_timepoint:35
SA326636	F83_35	RFT \| collection_timepoint:35
SA326637	F66_35	RFT \| collection_timepoint:35
SA326638	F80_35	RFT \| collection_timepoint:35
SA326639	F77_35	RFT \| collection_timepoint:35
SA326640	F76_35	RFT \| collection_timepoint:35
SA326641	F73_35	RFT \| collection_timepoint:35
SA326642	F75_56	RFT \| collection_timepoint:56
SA326643	F73_56	RFT \| collection_timepoint:56
SA326644	F76_56	RFT \| collection_timepoint:56
SA326645	F77_56	RFT \| collection_timepoint:56
SA326646	F80_56	RFT \| collection_timepoint:56
SA326647	F79_56	RFT \| collection_timepoint:56
SA326648	F70_56	RFT \| collection_timepoint:56
SA326649	F69_56	RFT \| collection_timepoint:56
SA326650	F66_56	RFT \| collection_timepoint:56
SA326651	F67_56	RFT \| collection_timepoint:56
SA326652	F83_56	RFT \| collection_timepoint:56
SA326653	F68_56	RFT \| collection_timepoint:56
SA326654	F49_0	RMT \| collection_timepoint:0
SA326655	F41_0	RMT \| collection_timepoint:0
SA326656	F48_0	RMT \| collection_timepoint:0
SA326657	F52_0	RMT \| collection_timepoint:0

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Collection:

Collection ID:	CO003107
Collection Summary:	In this study, 36 newborn calves were randomly assigned to three groups and followed for two months after birth. The groups included a control group (CON), a rumen microbiota transplantation group (RMT), and a rumen fluid transplantation group (RFT) and intensive data has been collected. The newborn calves were trained to feed milk using a bucket and then transferred to individual calf hutches. Starter was provided ad libitum three days after birth and once daily in the morning thereafter. Pasteurized whole milk was fed twice daily at 0800 and 1800 h using a bucket, and the calves were weaned 56 days after birth. RMT and RFT were performed by veterinarians, where the ruminal fluid used in RMT and RFT was collected from a healthy cattle (4-year-old, 600kg, in the dry period,) with a permanent rumen cannula 2 hours after the morning feed. Fresh ruminal fluid was mixed with raw milk and fed to the calves in the RMT group immediately after collection. For the RFT group, the ruminal fluid was autoclaved before feeding. A volume of 50 mL, 80 mL, and 110 mL of ruminal fluid was fed from day 7 to day 11, day 21 to day 25, and day 42 to day 46, respectively. Fecal and blood samples were collected at 15, 35, and 56 days after birth.
Collection Protocol Filename:	collection_protocol.docx
Sample Type:	Blood (plasma)

Treatment:

Treatment ID:	TR003123
Treatment Summary:	The newborn calves were trained to feed milk using a bucket and then transferred to individual calf hutches. Starter was provided ad libitum three days after birth and once daily in the morning thereafter. Pasteurized whole milk was fed twice daily at 0800 and 1800 h using a bucket, and the calves were weaned 56 days after birth. RMT and RFT were performed by veterinarians, where the ruminal fluid used in RMT and RFT was collected from a healthy cattle (4-year-old, 600kg, in the dry period,) with a permanent rumen cannula 2 hours after the morning feed. Fresh ruminal fluid was mixed with raw milk and fed to the calves in the RMT group immediately after collection. For the RFT group, the ruminal fluid was autoclaved before feeding. A volume of 50 mL, 80 mL, and 110 mL of ruminal fluid was fed from day 7 to day 11, day 21 to day 25, and day 42 to day 46, respectively. Fecal and blood samples were collected at 15, 35, and 56 days after birth.
Treatment Protocol Filename:	treatment_protocol.docx

Sample Preparation:

Sampleprep ID:	SP003120
Sampleprep Summary:	-
Sampleprep Protocol Filename:	sampleprep_protocol.docx

Combined analysis:

Analysis ID	AN004929
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Thermo Vanquish
Column	Thermo Hypersil GOLD aQ (100 x 2.1mm,1.9um)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Q Exactive HF hybrid Orbitrap
Ion Mode	UNSPECIFIED
Units	s

Chromatography:

Chromatography ID:	CH003720
Methods Filename:	UHPLC-MSMS_Analysis.docx
Instrument Name:	Thermo Vanquish
Column Name:	Thermo Hypersil GOLD aQ (100 x 2.1mm,1.9um)
Column Temperature:	40℃
Flow Gradient:	2% B, 1.5 min; 2-85% B, 3 min; 100% B, 10 min；100-2% B, 10.1 min；2% B, 12 min
Flow Rate:	0.2 mL/min
Solvent A:	100% water; 0.1% formic acid
Solvent B:	100% methanol
Chromatography Type:	Reversed phase

MS:

MS ID:	MS004672
Analysis ID:	AN004929
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Q ExactiveTM HF mass spectrometer was operated in positive/negative polarity mode with spray voltage of 3.2 kV, capillary temperature of 320°C, sheath gas flow rate of 40 arb and aux gas flow rate of 10 arb, Funnel RF level of 40, Aux gas heater temperature of 350°C.
Ion Mode:	UNSPECIFIED