GEO DataSets

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23295

10 Samples

Download data: TXT

(Submitter supplied) This comparative transcriptomic study examines the differences in the gene expression profile in PBMCs from indigenous Sahiwal and Crossbred (Sahiwal x Holstein Friesian) cattle in response to Infection with virulent Mycobacterium tuberculosis and vaccine stain M. bovis BCG.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

18 Samples

Download data: TXT

(Submitter supplied) Whole RNA transcriptome were performed on bovine lung cell 3D pulmosphere cultures with or without infection with M. bovis BCG and M. tuberculosis H37Rv strain.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

9 Samples

Download data: TXT

(Submitter supplied) Bovine Herpesvirus 1 (BoHV1) is a leading cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Therefore, the objective of the current study was to elucidate the cranial lung lobe mRNA transcriptomic response to an experimental challenge with BoHV1, in dairy calves. Holstein-Friesian calves were either challenged by intranasal atomisation with BoHV1 virus (6.3 x 10^7/mL x 1.35mL) (n=12) or mock challenged with sterile phosphate buffered saline (n=6). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

29 Samples

Download data: TXT

(Submitter supplied) Bovine Herpesvirus 1 (BoHV1) is a leading cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Therefore, the objective of the current study was to elucidate the bronchial lymph node mRNA transcriptomic response to an experimental challenge with BoHV1, in dairy calves. Holstein-Friesian calves were either challenged by intranasal atomisation with BoHV1 virus (6.3 x 10^7/mL x 1.35mL) (n=12) or mock challenged with sterile phosphate buffered saline (n=6). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

18 Samples

Download data: TXT

(Submitter supplied) Bovine Herpesvirus 1 (BoHV1) is a leading cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Therefore, the objective of the current study was to elucidate the mRNA transcriptomic response in mediastinal lymph node tissue to an experimental challenge with BoHV1, in dairy calves. Holstein-Friesian calves were either challenged by intranasal atomisation with BoHV1 virus (6.3 x 10^7/mL x 1.35mL) (n=12) or mock challenged with sterile phosphate buffered saline (n=6). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

18 Samples

Download data: TXT

(Submitter supplied) Bovine Herpesvirus 1 (BoHV1) is a leading cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Therefore, the objective of the current study was to elucidate the mRNA transcriptomic response in pharyngeal tonsil tissue to an experimental challenge with BoHV1, in dairy calves. Holstein-Friesian calves were either challenged by intranasal atomisation with BoHV1 virus (6.3 x 10^7/mL x 1.35mL) (n=12) or mock challenged with sterile phosphate buffered saline (n=6). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

18 Samples

Download data: TXT

(Submitter supplied) Bovine mammosphere-derived epithelial cells are a population with reported stem cell-like properties. We assessed these cells using scRNA-seq for markers of pluripotency and other features associated with the effects of their conditioned medium (CM).

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32030

1 Sample

Download data: MTX, TSV

(Submitter supplied) In this study, we established bovine embryonic stem cell (bESC) lines from early (eBL) and full (BL) blastocysts to determine the efficiency of bESC derivation from an earlier embryonic stage and compare the characteristics of the resulting lines. Using established medium and protocols for derivation of primed bESCs from expanded blastocysts, we derived bESC lines from eBLs and BLs with the same efficiency (4/12 each, 33%). more...

Organism:

Bos taurus; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL23295 GPL26012

9 Samples

Download data: TXT

(Submitter supplied) Here we report the derivation and long-term culture of bovine extraembryonic endoderm cells (bXENs). We showed that bXENs enhance maintain the stemness of bovine ESCs and prevent them from differentiation. In the present of signaling cocktail sustaining bXENs, the growth and progression of epiblasts are also facilitated in the developing pre-implantation embryo. Through 3D assembly of bXENs with bovine ESCs and TSCs, we developed an improved bovine blastocyst like structure (bovine blastoid). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

2 Samples

Download data: MTX, TSV

(Submitter supplied) Here we report the derivation and long-term culture of bovine extraembryonic endoderm cells (bXENs). The transcriptomic and epigenomic analyses confirmed the identity of bXENs and revealed that they are resemble for hypoblast cells of early bovine peri-implantation embryos.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL35143

6 Samples

Download data: BW, CSV

(Submitter supplied) The rumen plays an essential role in ruminant digestion, absorption, metabolism, and health. The rumen undergoes substantial changes in size and function from birth to adulthood. The molecular mechanisms underlying these changes are not fully understood. This study was aimed to identify the transcription factors and signaling pathways mediating these changes in cattle. We used 6 neonatal bull calves and 6 adult steers, all Angus-crossbred, in this study. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

8 Samples

Download data: TXT, XLSX

(Submitter supplied) PI3K-AKT signaling is essential for various cellular processes, including cell viability, proliferation, and metabolism. Here, we investigated the genome-wide changes induced by PI3K-AKTsignaling in primary granulosa cell cultures treated with control (DMSO) and PI3K-AKT pathway inhibitor LY294002.

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL16500

6 Samples

Download data: CEL

(Submitter supplied) Mycoplasma bovis mastitis is becoming increasingly problematic for dairy cattle farming in different parts of the world. M. bovis is inherently resistant to several antimicrobial classes and there is no effective vaccine. The major constraints to developing effective control tools are limited knowledge of M. bovis virulence factors and the underlying pathogenic mechanisms. The objective of this study was to determine virulence-associated genes of M. more...

Organism:

Mycoplasmopsis bovis; Bos taurus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34563 GPL26012 GPL34562

10 Samples

Download data: XLSX

(Submitter supplied) The SLICK1 allele of the prolactin receptor gene (SLICK1) is associated with a short hair coat and thermotolerance in cattle. SLICK1 includes a single base pair deletion that creates a premature stop codon and prevents transcription of 120 amino acids involved in JAK/STAT signaling. It is unknown if SLICK1 modifies JAK/STAT signaling or the transcriptional response to prolactin. To investigate PRLR-associated signaling pathways in heterozygous SLICK1+/- Holsteins (slick), we performed immunohistochemistry on skin explants obtained from slick (n=5) and non-slick (n=6) heifers to evaluate phosphorylated (p)STAT1, pSTAT3, and pSTAT5 immunoreactivity (pSTAT1+, pSTAT3+, pSTAT5+) in hair follicles (HF) and sweat glands (SG). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

12 Samples

Download data: TXT

(Submitter supplied) The new use of automated tools in assisted reproductive techniques rises the concern of a posible detrimental effect on development. In the current study there are no meaningful differences between the transcriptomes of bovine blastocysts produced in vitro following manual or automatic denudation of the presumptive zygotes after in vitro fertilization.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23295

15 Samples

Download data: CSV

(Submitter supplied) We developed an adapted version of Smart-seq2, which we call Smart-seq+5', to capture both internal transcript fragments, as well as 5' transcript information, in mammalian preimplantation stages on a single-embryo level. Focussing specifically on transposable elements, we find many conserved patterns and features shared between mouse, pig, cow, rabbit and rhesus.

Organism:

Sus scrofa; Macaca mulatta; Bos taurus; Mus musculus; Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

6 related Platforms

361 Samples

Download data: BW, TXT

(Submitter supplied) Developing embryos are susceptible to fluctuations in the nutrients and metabolites concentrations within the reproductive tract, which can lead to alterations in their developmental trajectory. Ketotic dairy cows have diminished fertility, and elevated levels of the ketone body beta-hydroxybutyrate (BHB) have been associated with poor embryonic development. We used an in vitro model based on either in vitro fertilization (IVF) or parthenogenesis to investigate the effects of BHB on the preimplantation bovine embryo development, epigenome, and transcriptome. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

6 Samples

Download data: CSV

(Submitter supplied) Progesterone (P4) is predicted to act as a negative regulatory hormone for oocyte maturation events; however, its local effects during follicular development remain poorly understood in bovine. The complex process of oocyte meiosis progression is dependent on cellular communication among follicular cells. Besides, the breakdown of this communication, mainly between cumulus cells and oocyte, through the retraction of cumulus projections connecting these cells can impact oocyte maturation. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

16 Samples

Download data: TXT

(Submitter supplied) A single Day-7 in vivo or in vitro-produced bovine embryo differentially modifies the endometrial transcriptome and the miRNA content in the released sEVs, which can also lead to modifications in the miRNA profile of luteal cells.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19172

29 Samples

Download data: CSV