GEO DataSets

(Submitter supplied) Objective: Classify and further validate BRD-associated genes and mechanisms found to be differentially expressed at facility arrival in post-weaned beef cattle from multiple independent populations. Our approach was to profile and compare at-arrival whole blood transcriptomes of post-weaned beef cattle that failed to develop symptoms associated with clinical BRD and cattle that ultimately were diagnosed and treated for clinical BRD within the first 28 days of facility arrival, further stratifying diseased animals into severity cohorts. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

48 Samples

Download data: GTF, TXT

(Submitter supplied) The objective of this study was to corroborate the findings of previous BRD-associated transcriptome experiments, utilizing multiple independent populations of high-risk beef cattle.

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL30354

240 Samples

Download data: RCC

(Submitter supplied) Objectives: Identify gene products that characterize the biological status of typical calves which have been recently weaned, transported, and co-mingled prior to arrival at stocker facilities in order to identify gene products associated with BRD resistance. Methods: Whole blood RNA profiles were generated via NGS approach, using an Illumina HiSeq 3000. Individual samples were processed using an adaptation of the Revised Tuxedo Suite protocol (Tuxedo 2), then analyzed in R using edgeR and DESeq2 with likelihood-ratio testing. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21659

12 Samples

Download data: GTF, TXT

(Submitter supplied) Jugular whole blood samples (Tempus Blood RNA tubes) were collected and utilized from 43 cattle, specifically from all cattle diagnosed with bovine respiratory disease (BRD) during Texas backgrounding (n=32) and randomly selected cattle never treated for BRD (n=11). Total RNA was isolated from blood samples, and were library prepared and sequenced via Illumina NovaSeq 6000 S4 chemistry. Samples were bioinformatically processed in a HISAT2/StringTie2 pipeline, and stratified based on BRD diagnosis and marketing strategy (Auction versus Direct marketing and transport). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

43 Samples

Download data: TXT

(Submitter supplied) To evaluate how commonly-utilized antimicrobials affect the host transcriptome of commercial beef cattle overtime, we enrolled 105 feedlot beef steers randomly into seven different treatment groups (negative control, tulathromycin, tildipirosin, enrofloxacin, florfenicol, ceftiofur, oxytetracycline) to receive a one-time label dose of a commercial antimicrobial or not (negative control), and collected jugular whole blood into PAXgene RNA blood tubes at six time points: Day 0 (baseline), 3, 7, 14, 21, and 56.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

252 Samples

Download data: TXT

(Submitter supplied) In this study we aimed to identify differentially expressed (DE) genes involved in the host immune response to BRD using whole blood and RNA sequencing. Samples were collected from heifers (average arrival weight = 215.0 ± 5.3 kg) with (n = 25) and without (n = 18) BRD at a commercial feedlot in Western Canada. RNAseq analysis showed a distinct whole blood transcriptomic profile between BRD and non-BRD heifers. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23295

43 Samples

Download data: CSV

(Submitter supplied) The study investigated gene expression patterns in liver tissue to understand the biological functions of genes that are potentially involved in controlling / regulating feed efficiency in Nordic dairy cattle.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19172

38 Samples

Download data: TXT

(Submitter supplied) Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in calves over one month of age. In a controlled challenge study in artificially-reared dairy calves, the influence of the host response to bovine respiratory syncytial virus (BRSV) was examined. Holstein-Friesian calves were either inoculated with BRSV (10^5/ml × 15 ml/animal) (n=12) or mock challenged with phosphate buffer saline (10ml/animal) (n=6). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

18 Samples

Download data: CSV

(Submitter supplied) Bovine Respiratory Syncytial Virus (BRSV) is a leading cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Infection with BRSV induces global gene expression changes in respiratory tissues. If these changes are observed in tissues which are accessible in live animals, such as whole blood, they may be used as biomarkers of the disease. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

18 Samples

Download data: TXT

(Submitter supplied) Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). The objective of this study was to elucidate the chromatin regions which were differentially open in the bronchial lymph nodes (BLN) of dairy calves experimentally challenged with BRSV, relative to unchallenged control calves. Holstein-Friesian calves were either challenged with BRSV inoculum (n=12) or mock challenged with PBS (n=6). more...

Organism:

Bos taurus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23055

18 Samples

Download data: NARROWPEAK

(Submitter supplied) Bovine respiratory disease (BRD) is the most common and costly infectious disease affecting the well-being and productivity of beef cattle in North America. BRD is a complex disease whose development is dependent on environmental factors and host genetics. Due to the polymicrobial nature of BRD, our understanding of the genetic and molecular mechanisms underlying the disease is still limited. This knowledge would augment the development of better genetic/genomic selection strategies and more accurate diagnostic tools to reduce BRD prevalence. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26012 GPL23295

143 Samples

Download data: CSV

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

Organism:

Bos taurus

Type:

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

Platform:

GPL15749

50 Samples

Download data

(Submitter supplied) The regulation of endometrial inflammation has important consequences for the resumption of bovine fertility post-partum. All cows experience bacterial influx into the uterus after calving; however a significant proportion fail to clear infection leading to the development of cytological endometritis (CE) and compromised fertility. We hypothesised that early immunological changes could not only act as potential prognostic biomarkers for the subsequent development of disease but also shed light on the pathogenesis of endometritis in the post-partum dairy cow. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15749

20 Samples

Download data: TXT

(Submitter supplied) The regulation of endometrial inflammation has important consequences for the resumption of bovine fertility post-partum. All cows experience bacterial influx into the uterus after calving; however a significant proportion fail to clear infection leading to the development of cytological endometritis (CE) and compromised fertility. We hypothesised that early immunological changes could not only act as potential prognostic biomarkers for the subsequent development of disease but also shed light on the pathogenesis of endometritis in the post-partum dairy cow. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15749

30 Samples

Download data: TXT