GEO DataSets

(Submitter supplied) Despite buffaloes being primary farm animals, their reproductive performance remains poor mainly due to inaccurate estrus detection methods that ultimately has an economic impact on dairy industry as well as farmers. Recently, numerous studies showed potential of miRNAs as estrus biomarker. However, a miRNA profile of buffalo cell free saliva, a non-invasive fluid, at estrus and diestrus stages is missing. more...

Organism:

Bubalus bubalis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL31047

6 Samples

Download data: CSV

(Submitter supplied) To investigate the function lncFABP4 in the regulation of adipogenic differentiation, we overexpressed lncFABP4 in buffalo intramuscular adipocytes

Organism:

Bubalus bubalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33338

6 Samples

Download data: FA, XLSX

(Submitter supplied) RNA Seq data showed 49 differentially altered mRNAs in estrus and diestrus stages of buffalo cell free saliva, that includes 10 mRNAs commonly present in both estrus and diestrus stages, whereas 12 and 27 mRNAs were found to be exclusively present either at the estrus or the diestrus stage respectively. In addition, four mature miRNAs were predicted to be differentially altered in the estrus as compared to the diestrus phase of buffaloes.

Organism:

Bubalus bubalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29600

2 Samples

Download data: XLSX

(Submitter supplied) To characterize the transcriptome differences between different adipose depots, a total of 36 adipose samples were used for high-throughput sequencing. At last, about 23,000 transcripts were identified.

Organism:

Bubalus bubalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26105

36 Samples

Download data: FA, XLSX

(Submitter supplied) Feed regimens have a pivotal role in modulating the transcriptional programs that, in turns, have an impact on many biological processes, including metabolism, health and development. Green feed diet in ruminant exerts a beneficial effect on rumen metabolism and enhances the content of health-promoting biomolecules in the milk. However, a comprehensive analysis focused to the identification of genes, and therefore, biological processes modulated by the green feed diet in buffalo rumen has never been reported so far. more...

Organism:

Bubalus bubalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31047

12 Samples

Download data: TXT

(Submitter supplied) Spermatogenesis carries the task of precise intergenerational transmission of genetic information from the paternal genome and involves complex developmental processes regulated by the testicular microenvironment. Studies performed mainly in mouse models have established the theoretical basis for spermatogenesis, yet the wide inter-species differences preclude direct translation of the findings, and farm animal studies are progressing slowly. more...

Organism:

Bubalus bubalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31047

2 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) The long reproductive cycle of buffalo is a key factor limiting the expansion of buffalo populations. Early and accurate pregnancy diagnosis in breeding heifers can shorten calving intervals and improve reproductive efficiency. Circular RNA (circRNA) is expressed in cells and tissues of several species. However, the expression of circRNAs in the blood of Jianghuai buffaloes during early pregnancy has not been reported. more...

Organism:

Bubalus bubalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29600

6 Samples

Download data: XLSX

(Submitter supplied) Background: Intramuscular fat (IMF) content is an important index for beef quality. However, the genetics of IMF deposition is complex and still largely unclear, especially in buffalo. To identify miRNAs with potential regulatory role in lipid accumulated in muscle, we performed small RNA sequencing and identified miRNAs expressed in the longissimus dorsi muscle and back fat of Chinese buffalo, which provided vital information for further identification of miRNAs with potential regulatory role in the lipid accumulated in muscle. more...

Organism:

Bubalus bubalis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25494

3 Samples

Download data: FA, XLS

(Submitter supplied) Background: Intramuscular fat (IMF) content is an important index for beef quality. However, the genetics of IMF deposition is complex and still largely unclear, especially in buffalo. To identify miRNAs with potential regulatory role in lipid accumulated in muscle, we performed small RNA sequencing and identified miRNAs expressed in the longissimus dorsi muscle and back fat of Chinese buffalo, which provided vital information for further identification of miRNAs with potential regulatory role in the lipid accumulated in muscle. more...

Organism:

Bubalus bubalis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25494

6 Samples

Download data: FA, TXT

(Submitter supplied) Buffalo breeding has become an important branch of beef cattle industry. It is of great significance to study buffalo meat production and meat quality. However, the important role of mRNA and lncRNA molecules in muscle stem cells (MuSCs) development in buffalo has not been explored. Then, we performed mRNA and lncRNA expression profiling analysis on the proliferation and differentiation of MuSCs in buffalo. more...

Organism:

Bubalus bubalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29600

6 Samples

Download data: TXT

(Submitter supplied) Compared with granulosa cells from healthy follicles, 2888 (1790 up-regulated, 1098 down-regulated) and 1629 (1230 up-regulated, 399 down-regulated) DEGs (|FC| > 1.75 and P value < 0.05) were identified in granulosa cells of early atretic follicles and late atretic follicle, respectively. Out of these DEGs, 1217 genes were commonly shared among the two comparisons

Organism:

Bubalus bubalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29600

9 Samples

Download data: XLS

(Submitter supplied) GCs were collected from HFs and AFs , to use second-generation high-throughput sequencing for whole-transcriptome analysis, respectively. In total, 1861 and 1075 mRNAs, 159 and 24 miRNAs, 123 and 100 lncRNAs, and 58 and 54 circRNAs were identified to be differentially expressed (DE) in up-regulated and down-regulated. Enrichment of functions and signaling pathways of the DEgenes showed that most of DEmRNAs and targets of DEmiRNAs, DElncRNAs and DEcricRNAs were annotated to the categories of ‘PI3K-Akt signaling pathway’, ‘ECM-receptor interaction’, ‘Focal adhesion’, ‘mTOR signaling pathway ’ ‘TGF-beta signaling pathway’, ‘Rap1 signaling pathway’, and ‘Estrogen signaling pathway’. more...

Organism:

Bubalus bubalis

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL26105

6 Samples

Download data: XLS

(Submitter supplied) Background: Intramuscular fat (IMF) content is highly valued as it improves meat product quality by enhancing taste, juiciness, and tenderness. IMF content can be significantly different between breeds. Thought many lipid metabolism-related genes are stated to be associated with IMF deposition, the molecular mechanism of IMF deposition is still poorly understood. To date, no gene or mutation loci responsible for the difference of IMF content among cattle breeds has been identified. more...

Organism:

Bubalus bubalis; Bos taurus

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL24849 GPL21659

9 Samples

Download data: FA, XLS

(Submitter supplied) We report the distribution of histone acetylation at global genomic level in donor cells with different cloning efficiency. By obtaining over 40 million clean reads from immunoprecipitated DNA, we generated genome-wide chromatin-state maps of two buffalo fibroblast cell lines. We find that high cloning efficiency BFFs also had more regions enriched with H3K9ac sites near to the upstream of genes related to glycolysis. more...

Organism:

Bubalus bubalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24849

6 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bubalus bubalis

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26105

16 Samples

Download data

(Submitter supplied) Purpose: To investigate whether FgESP affects the hydroxylmethylation level of DCs Methods: we have profiled the DNA hydroxymethylome by using hydroxymethylated DNA immunoprecipitation sequencing (h)MeDIP-Seq in the current study Results: DNA hydroxymethylation profiles revealed significant changes in the 5-hydroxymethylcytosine (5hmC) levels in 360 genes when DCs were treated with FgESPs. These differentially expressed genes were highly enriched in pathways associated with immune function. more...

Organism:

Bubalus bubalis

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26105

8 Samples

Download data: XLSX

(Submitter supplied) Purpose: To investigate whether FgESP affects the (hydroxyl)methylation level of DCs Methods: we have profiled the DNA methylome by using methylated DNA immunoprecipitation sequencing (MeDIP-Seq) in the current study Results: DNA methylation and hydroxymethylation profiles revealed significant changes in the 5-methylcytosine (5-mC) levels in the promoter regions of 5432 genes and significant changes in the 5-hydroxymethylcytosine (5hmC) levels in 360 genes when DCs were treated with FgESPs. more...

Organism:

Bubalus bubalis

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26105

8 Samples

Download data: XLSX

(Submitter supplied) Background: Background: In bovines, the development and growth of adipose involves many physiological processes and plays an extremely important role in the quality of beef, however, the regulatory mechanisms underlying the differences in meat quality are largely unknown. Therefore, a buffalo adipose transcriptome analysis was performed to compare gene expression profiles between different growth stages. more...

Organism:

Bubalus bubalis

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24849

6 Samples

Download data: FA, XLS, XLSX

(Submitter supplied) Duplicated sequences are the important source of gene innovation and structural variation within mammalian genomes. Using a read depth approach based on next-generation sequencing, we performed a genome-wide analysis of segmental duplications (SDs) and associated copy number variants (CNVs) in water buffalo (Bubalus bubalis). Aligning to the UMD3.1 cattle genome, we estimated 44.6 Mb (~1.73% of cattle genome) segmental duplications in the autosomes and X chromosome using the sequencing reads of Olimpia (the sequenced water buffalo). more...

Organism:

Bubalus bubalis

Type:

Genome variation profiling by genome tiling array

Platform:

GPL25422

14 Samples

Download data: TXT

(Submitter supplied) Background:Maternal mRNAs that accumulate in the oocyte during oogenesis play important roles during initial stages of embryonic development, before activation of the embryonic genome. Parthenogenesis of mammalian is a critical research modle for the function analysis of maternal genomics. Results:Here we report comprehensive maternal transcriptome dynamics of single matured oocytes and pre-implantation embryos of buffalo parthenogenesis.Notably, more than half of the estimated 28659 bovine genes,15331 involved in more than 280 pathways, is expressed in oocytes and early embryos of parthenogenesis .The total numbers of genes expressed across stages are from 908 genes (morula/16cells)to 2603 genes(blastocyst/morula), and the nature of the expressed genes is also greatly different. more...

Organism:

Bubalus bubalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24447

8 Samples

Download data: FA, XLS