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.
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 | ST003745 |
| Study Title | Screen potential marker proteins influencing spermatogenesis in the testes of Shandong Black Cattle bulls via multi-omics integrated analysis. |
| Study Summary | This 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 Name | DONG |
| First Name | YA JUAN |
| Address | 700 Changcheng Road, Chengyang District |
| etcenter@126.com | |
| Phone | 13561688666 |
| Submit Date | 2025-02-16 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-03-09 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
