Summary of Study ST003745

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 PR002331. The data can be accessed directly via it's Project DOI: 10.21228/M8B246 This work is supported by NIH grant, U2C- DK119886.

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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 IDST003745
Study TitleScreen potential marker proteins influencing spermatogenesis in the testes of Shandong Black Cattle bulls via multi-omics integrated analysis.
Study SummaryThis study was designed to identify candidate marker proteins that influence the growth and development of Shandong Black Cattle bull testes through a multi-omics joint analysis, thereby providing a certain theoretical basis for testis growth and development as well as bull selection. Eight 12-month-old Shandong Black Cattle bulls were selected, and testes tissues were collected. The testes were categorized into two groups based on their morphological characteristics: Group 1 (weight > 120 g) and Group 2 (weight < 120 g). Group 2 was employed as the control group to construct a protein and metabolite library for joint analysis to screen candidate marker proteins that affect testis growth and development. The results revealed that 1553 differential proteins (DEPs) were differentially expressed between the large and small testes of Black Bleykett bulls, with 1219 being upregulated and 334 being downregulated. The KEGG enrichment results manifested that the upregulated DEPs were primarily involved in the cell cycle (CDK1, CCNB, MCM4), DNA replication (MCM3, MCM4), etc. The downregulated DEPs were mainly associated with metabolic pathways (ACSM1, IMPDH1), etc. The GO enrichment results disclosed that the DEPs were significantly enriched in the categories of cytoskeleton movement. The weighted gene co-expression analysis suggested that the testis weight was significantly correlated with MCM, STRADA, and SEC31B. After integrating the DEPs, a PPI analysis was performed, and 10 key regulatory proteins were identified, including MCM3, MCM4, CDK1, and CDK2. Metabolomics demonstrated that 59 upregulated metabolites were enriched in the glucose metabolism pathway (uridine diphosphate glucose), and 14 downregulated metabolites were significantly enriched in metabolic pathways (hypoxanthine).
Institute
Qingdao Agricultural University
Last NameDONG
First NameYA JUAN
Address700 Changcheng Road, Chengyang District
Emailetcenter@126.com
Phone13561688666
Submit Date2025-02-16
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2025-03-09
Release Version1
YA JUAN DONG YA JUAN DONG
https://dx.doi.org/10.21228/M8B246
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002331
Project DOI:doi: 10.21228/M8B246
Project Title:Screen potential marker proteins influencing spermatogenesis in the testes of Shandong Black Cattle bulls via multi-omics integrated analysis.
Project Summary:Testes tissue was collected from 8 12-month-old Shandong black cattle. Testes were divided into two groups according to the morphological characteristics of testes: group 1 (weight > 120 g) and group 2 (weight < 120 g). With group 2 as the control group, protein and metabolite libraries were constructed for joint analysis, and candidate marker proteins affecting testes growth and development were screened. It provides some theoretical basis for testes growth and development and selection of bulls. The results revealed that 1553 differential proteins (DEPs) were differentially expressed between the large and small testes of Black Bleykett bulls, with 1219 being upregulated and 334 being downregulated. Metabolomics demonstrated that 59 upregulated metabolites were enriched in the glucose metabolism pathway (uridine diphosphate glucose), and 14 downregulated metabolites were significantly enriched in metabolic pathways (hypoxanthine).
Institute:Qingdao Agricultural University
Last Name:DONG
First Name:YA JUAN
Address:700 Changcheng Road, Chengyang District
Email:etcenter@126.com
Phone:13561688666

Subject:

Subject ID:SU003878
Subject Type:Mammal
Subject Species:Bos taurus
Taxonomy ID:9913
Gender:Male

Factors:

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

mb_sample_id local_sample_id Sample source Group
SA408205G01970-2Testis Control
SA408206G01994-2Testis Control
SA408207G01994-1Testis Control
SA408208G06650-2Testis Control
SA408209G06650-1Testis Control
SA408210G06649-2Testis Control
SA408211G06649-1Testis Control
SA408212G06970-2Testis Control
SA408213G06970-1Testis Control
SA408214G01970-1Testis Control
SA408215G01987-2Testis Normal
SA408216G01952-2Testis Normal
SA408217G01987-1Testis Normal
SA408218G06733-2Testis Normal
SA408219G06733-1Testis Normal
SA408220G01977-2Testis Normal
SA408221G01977-1Testis Normal
SA408222G01957-1Testis Normal
SA408223G01957-2Testis Normal
SA408224G01952-6Testis Normal
SA408225G01952-5Testis Normal
SA408226G01952-4Testis Normal
SA408227G01952-3Testis Normal
SA408228G01952-1Testis Normal
Showing results 1 to 24 of 24

Collection:

Collection ID:CO003871
Collection Summary:Testicular samples were collected and their weight, long diameter and wide diameter were measured. The testes were categorized into two groups based on their morphological characteristics: Group 1 (weight > 120 g) and Group 2 (weight < 120 g), with 4 animals in each group. Group 1 was designated as the Normal group and Group 2 was employed as the control group. The testicular samples were stored in liquid nitrogen and paraformaldehyde.An independent sample t-test revealed significant differences (P < 0.05) between the two groups in terms of body weight, testis weight, testis width, and testis length . The most pronounced difference was observed in testis weight, with the G1 group exhibiting a testis weight 1.8 times greater than that of the G2 group.In contrast, differences in testis width and length were relatively smaller, with each measurement in the G1 group being approximately 1.2 times that of the G2 group.Notably, the G2 group had a body weight 1.1 times higher than that of the G1 group at 0d.
Sample Type:Testes

Treatment:

Treatment ID:TR003887
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP003884
Sampleprep Summary:Tissues (100 mg) were individually grounded with liquid nitrogen and the homogenate was resuspended with 500μL prechilled 80% methanol by well vortex. The samples were incubated on ice for 5 min and then were centrifuged at 15,000 g, 4°C for 20 min. Some of supernatant was diluted to final concentration containing 53% methanol by LC-MS grade water. The samples were subsequently transferred to a fresh Eppendorf tube and then were centrifuged at 15000 g, 4°C for 20 min. Finally, the supernatant was injected into the LC-MS/MS system analysis

Combined analysis:

Analysis ID AN006150 AN006151
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish
Column Thermo Hypersil GOLD C18 (100 x 2.1mm,1.9um) Thermo Hypersil GOLD C18 (100 x 2.1mm,1.9um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF-X Orbitrap Thermo Q Exactive HF-X Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Peak area Peak area

Chromatography:

Chromatography ID:CH004671
Chromatography Summary:Positive: UHPLC-MS/MS analyses were performed using a Vanquish UHPLC system (ThermoFisher, Germany) coupled with an Orbitrap Q ExactiveTM HF-X mass spectrometer (Thermo Fisher，Germany) in Gene Denovo Co., Ltd. (Guangzhou, China). Samples were injected onto a Hypesil Gold column (100×2.1 mm, 1.9μm) using a 17-min linear gradient at a flow rate of 0.2mL/min. The eluents for the positive polarity mode were eluent A (0.1% FA in Water) and eluent B(Methanol).The eluents for the negative polarity mode were eluent A (5 mM ammonium acetate, pH 9.0) and eluent B (Methanol).The solvent gradient was set as follows: 2% B, 1.5 min; 2-100% B, 12.0 min; 100% B, 14.0 min；100-2% B, 14.1 min；2% B, 17min.
Instrument Name:Thermo Vanquish
Column Name:Thermo Hypersil GOLD C18 (100 x 2.1mm,1.9um)
Column Temperature:40℃
Flow Gradient:0.0-1.5 min at 2%B; 1.5-12min from 2%B to-100% B; 12.0 min; 12-14min at 100% B; 14.0-14.1 min from100%B to 2% B;14.1 -17min at 2% B
Flow Rate:0.2mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% methanol
Chromatography Type:Reversed phase
  
Chromatography ID:CH004672
Chromatography Summary:Negative: UHPLC-MS/MS analyses were performed using a Vanquish UHPLC system (ThermoFisher, Germany) coupled with an Orbitrap Q ExactiveTM HF-X mass spectrometer (Thermo Fisher，Germany) in Gene Denovo Co., Ltd. (Guangzhou, China). Samples were injected onto a Hypesil Gold column (100×2.1 mm, 1.9μm) using a 17-min linear gradient at a flow rate of 0.2mL/min. The eluents for the positive polarity mode were eluent A (0.1% FA in Water) and eluent B(Methanol).The eluents for the negative polarity mode were eluent A (5 mM ammonium acetate, pH 9.0) and eluent B (Methanol).The solvent gradient was set as follows: 2% B, 1.5 min; 2-100% B, 12.0 min; 100% B, 14.0 min；100-2% B, 14.1 min；2% B, 17min.
Instrument Name:Thermo Vanquish
Column Name:Thermo Hypersil GOLD C18 (100 x 2.1mm,1.9um)
Column Temperature:40℃
Flow Gradient:0.0-1.5 min at 2%B; 1.5-12min from 2%B to-100% B; 12.0 min; 12-14min at 100% B; 14.0-14.1 min from100%B to 2% B;14.1 -17min at 2% B
Flow Rate:0.2mL/min
Solvent A:100% water; 5mM ammonium acetatep H9.0
Solvent B:100% methanol
Chromatography Type:Reversed phase

MS:

MS ID:MS005855
Analysis ID:AN006150
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Q ExactiveTM HF-X mass spectrometer was operated in positive/negative polarity mode with spray voltage of 3.5 kV, Sheath gas flow rate: 35psi; Auxiliary gas flow rate (Aux Gas flow rate): 10L/min; Ion transfer tube temperature (Capillary Temp): 320°C; Ion introduction radio frequency level (S-lens RF level): 60; Auxiliary gas heater temperature (Aux gas heater temp): 350°C; Polarity: positive, negative; MS/MSsecondary scanning is data-dependent scanning
Ion Mode:POSITIVE
  
MS ID:MS005856
Analysis ID:AN006151
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Q ExactiveTM HF-X mass spectrometer was operated in positive/negative polarity mode with spray voltage of 3.5 kV, Sheath gas flow rate: 35psi; Auxiliary gas flow rate (Aux Gas flow rate): 10L/min; Ion transfer tube temperature (Capillary Temp): 320°C; Ion introduction radio frequency level (S-lens RF level): 60; Auxiliary gas heater temperature (Aux gas heater temp): 350°C; Polarity: positive, negative; MS/MSsecondary scanning is data-dependent scanning
Ion Mode:NEGATIVE
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