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 IDST003001
Study TitleThe Track Dairy Cattle (trackDC) study
Study SummaryThe 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 NameDong
First NameQuanbin
AddressNo. 215 Guangzhou road
Emailqbdong@stu.njmu.edu.cn
Phone15311095435
Submit Date2023-12-10
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-12-12
Release Version1
Quanbin Dong Quanbin Dong
https://dx.doi.org/10.21228/M8VX4G
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

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 collection_timepoint
SA326558F86_0CON 0
SA326559F84_0CON 0
SA326560F64_0CON 0
SA326561F87_0CON 0
SA326562F65_0CON 0
SA326563F89_0CON 0
SA326564F92_0CON 0
SA326565F91_0CON 0
SA326566F90_0CON 0
SA326567F63_0CON 0
SA326568F88_0CON 0
SA326569F62_0CON 0
SA326570F65_15CON 15
SA326571F63_15CON 15
SA326572F62_15CON 15
SA326573F92_15CON 15
SA326574F84_15CON 15
SA326575F64_15CON 15
SA326576F88_15CON 15
SA326577F91_15CON 15
SA326578F87_15CON 15
SA326579F89_15CON 15
SA326580F86_15CON 15
SA326581F90_15CON 15
SA326582F84_35CON 35
SA326583F92_35CON 35
SA326584F62_35CON 35
SA326585F91_35CON 35
SA326586F63_35CON 35
SA326587F64_35CON 35
SA326588F65_35CON 35
SA326589F87_35CON 35
SA326590F90_35CON 35
SA326591F88_35CON 35
SA326592F86_35CON 35
SA326593F89_35CON 35
SA326594F90_56CON 56
SA326595F89_56CON 56
SA326596F64_56CON 56
SA326597F92_56CON 56
SA326598F88_56CON 56
SA326599F91_56CON 56
SA326600F87_56CON 56
SA326601F63_56CON 56
SA326602F62_56CON 56
SA326603F84_56CON 56
SA326604F86_56CON 56
SA326605F65_56CON 56
SA326606F67_0RFT 0
SA326607F66_0RFT 0
SA326608F69_0RFT 0
SA326609F68_0RFT 0
SA326610F77_0RFT 0
SA326611F80_0RFT 0
SA326612F83_0RFT 0
SA326613F79_0RFT 0
SA326614F76_0RFT 0
SA326615F73_0RFT 0
SA326616F75_0RFT 0
SA326617F70_0RFT 0
SA326618F79_15RFT 15
SA326619F69_15RFT 15
SA326620F68_15RFT 15
SA326621F66_15RFT 15
SA326622F83_15RFT 15
SA326623F70_15RFT 15
SA326624F67_15RFT 15
SA326625F77_15RFT 15
SA326626F76_15RFT 15
SA326627F80_15RFT 15
SA326628F73_15RFT 15
SA326629F75_15RFT 15
SA326630F70_35RFT 35
SA326631F68_35RFT 35
SA326632F67_35RFT 35
SA326633F75_35RFT 35
SA326634F69_35RFT 35
SA326635F79_35RFT 35
SA326636F83_35RFT 35
SA326637F66_35RFT 35
SA326638F80_35RFT 35
SA326639F77_35RFT 35
SA326640F76_35RFT 35
SA326641F73_35RFT 35
SA326642F75_56RFT 56
SA326643F73_56RFT 56
SA326644F76_56RFT 56
SA326645F77_56RFT 56
SA326646F80_56RFT 56
SA326647F79_56RFT 56
SA326648F70_56RFT 56
SA326649F69_56RFT 56
SA326650F66_56RFT 56
SA326651F67_56RFT 56
SA326652F83_56RFT 56
SA326653F68_56RFT 56
SA326654F49_0RMT 0
SA326655F41_0RMT 0
SA326656F48_0RMT 0
SA326657F52_0RMT 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
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