Abstract
Cattleyak are hybrid between cattle and yak, which exhibit equivalent
adaptability on the Qinghai-Tibetan Plateau as yak and much higher
capability in economic traits. However, the F1 males of cattleyak are
infertile due to spermatogenic arrest and this greatly restricts the
effective utilization of this hybrid. In this data article,
differentially expressed proteins (DEPs) were identified from testis
proteome of cattleyak and yak using high-performance liquid
chromatography–electrospray tandem mass spectrometry (LC–ESI-MS/MS).
All the DEPs were subjected to functional classification by Gene
Ontology (GO) analysis and gene-pathway annotation by Kyoto
Encyclopedia of Genes and Genomes (KEGG). The comparative testis
proteome dataset here can shed new light on the molecular
characteristics of male infertility of cattleyak on proteome level,
“Comparative iTRAQ proteomics revealed proteins associated with
spermatogenic arrest of cattleyak” [31][1].
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Specifications Table
Subject area Biology
More specific subject area Reproductive biology
Type of data Table, figure
How data was acquired Mass spectroscopy, data acquired by LC–ESI-MS/MS
analysis based on Triple TOF 5600
Data format Analyzed
Experimental factors Testis of each animal was obtained by veterinary
surgical operation. Fat and fascia tissues surrounding the testis were
eliminated and were snap frozen in liquid nitrogen (−196 °C),
transported to laboratory and stored at −80 °C until analysis.
Experimental features Total protein was taken out of each sample
solution and was digested with Trypsin Gold (Promega, Madison, WI,
USA). After trypsin digestion, peptides were dried by vacuum
centrifugation and then reconstituted and processed according to the
manufacture׳s protocol for 8-plex iTRAQ reagent (Applied Biosystems).
SCX chromatography was performed with a LC-20AB HPLC Pump system
(Shimadzu, Kyoto, Japan). Data acquisition was performed with a
TripleTOF 5600 System (AB SCIEX, Concord, ON).
Data source location Mianyang, Sichuan, China
Data accessibility The data is available with this article
[32]Open in a new tab
Value of the data
* •
This is the first dataset to examine the male infertility of
cattleyak by comparative testis proteome.
* •
The dataset lays the basis for a clear presentation of up-regulated
proteins in cattleyak associated with various stresses/cell
adhesion/germ cell migration and down-regulated proteins associated
with defects in various metabolic processes/cellular processes
during spermatogenesis.
* •
The DEPs indicate their potential functions in spermatogenic arrest
in cattleyak.
1. Data
This data is related to DEPs from testis proteome of cattleyak and yak
using LC–ESI-MS/MS [33][1]. All the DEPs were categorized by GO and
KEGG analysis. See [34]Supplementary Figures and Tables provided.
2. Experimental design, materials and methods
2.1. Sample collection
The sampling of cattleyak and yak, and preparing of testis from each
animal was described in Reference [35][1].
2.2. Protein preparation
Each testicular sample was ground into powder by successively adding
liquid nitrogen in a mortar. Then each sample powder was extracted with
lysis buffer and the protein was prepared as described in Reference
[36][1].
2.3. iTRAQ Labeling and SCX fractionation
Total protein (100 μg) was extracted from each sample solution. After
digestion with Trypsin Gold (Promega, Madison, WI, USA), peptides from
each sample were dried and processed according to the manufacture׳s
protocol for 8-plex iTRAQ reagent (Applied Biosystems). SCX
fractionation was performed as description in Reference [37][1].
2.4. LC–ESI-MS/MS analysis based on Triple TOF 5600 and data analysis
The preparation of each SCX fraction, data acquisition and data
analysis were performed as description in Reference [38][1].
In total, 552 DEPs met the criteria for analysis (signal present in all
three biological replicates, minimum fold change of ±1.2 or greater and
p<0.05) by comparing of the testis proteome between cattleyak and yak,
in which 206 proteins were up-regulated ([39]Supplementary Table 1) and
346 ones ([40]Supplementary Table 2) were down-regulated in cattleyak
with respect to yak.
2.5. Gene ontology (GO) analysis of DEPs
GO enrichment analysis firstly maps all DEPs to GO terms in the
database ([41]http://www.geneontology.org/), calculating protein
numbers for every term. Hypergeometric test was employed to screen
significantly enriched GO terms from DEPs by using a strict algorithm
as follows:
[MATH: P=1−
∑i=0m−1(Mi)(N−Mn−i)(Nn) :MATH]
N denotes the number of all proteins and n denotes the number of DEPs
in N; M is the number of all proteins that are annotated to certain GO
terms and m denotes the number of DEPs in M. The p-value is subjected
to Bonferroni Correction, with the corrected p-value ≤0.05 as a
threshold. GO terms fulfilling this condition are defined as
significantly enriched GO terms in DEPs.
All DEPs (552) screened from testis proteome of cattleyak and yak were
analyzed by GO according to cellular component, molecular function, and
biological process. The 28 significantly enriched GO terms with respect
to cellular component were mainly associated with extracellular matrix
organization, collagen fibril organization and cytoplasmic part
[42][1]. In contrast, 56 significantly enriched GO terms were mainly
were involved in binding, transporter and oxidoreductase activity in
molecular function ([43]Fig. 1). Furthermore, 200 GO terms were
significantly enriched based on biological process and they were mainly
involved in extracellular matrix organization, germ cell development,
response to stimulus and metabolic process ([44]Supplementary Fig. 1).
Fig. 1.
[45]Fig. 1
[46]Open in a new tab
Significant GO terms of differentially expressed proteins on the basis
of molecular function. The x-axis and y-axis correspond to GO terms and
percent of genes, respectively. GO terms in each ontological category
were ranked according to increased p-value and listed on the x-axis
from left to right.
2.6. Pathway enrichment analysis of DEPs
KEGG (the major public pathway-related database) [47][2] is used to
identify significantly enriched metabolic pathways or signal
transduction pathways in DEPs comparing with certain proteome
background. Hypergeometric test was also employed to screen
significantly enriched pathways from DEPs by using a strict algorithm
as that in GO analysis. Here, N denotes the number of all proteins that
with KEGG annotation and n denotes the number of DEPs in N. M is the
number of all proteins annotated to specific pathways and m is the
number of DEPs in M.
In total, 465 DEPs were mapped to the reference pathways in KEGG
database and only 15 significantly enriched pathways were obtained
(p≤0.05), in which ECM-receptor interaction, Protein digestion and
absorption, Alzheimer׳s disease, Ribosome and Pentose phosphate pathway
were the top listed pathways [48][1]. Mitochondrial dysfunction
involved in such pathways as Alzheimer׳s disease ([49]Fig. 2) and
oxidative phosphorylation pathways ([50]Fig. 3) resulted from
downregulation of some proteins mitochondrial cytochrome complex may
lead to cell death in cattleyak testis.
Fig. 2.
[51]Fig. 2
[52]Open in a new tab
Differentially expressed proteins involved in the pathway of
Alzheimer׳s disease. Red-boxed proteins were upregulated and
green-boxed proteins were downregulated.
Fig. 3.
[53]Fig. 3
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Differentially expressed proteins involved in the pathway of oxidative
phosphorylation. Red-boxed proteins were upregulated and green-boxed
proteins were downregulated.
Acknowledgments