GEO DataSets

(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 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 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 Disease (BRD) is responsible for the majority of calf morbidity and mortality. One of the main causes of BRD is initial infection with Bovine Respiratory Syncytial Virus (BRSV). The objective of this study was to elucidate the changes in the host's bronchial lymph node miRNA transcriptome in response to BRSV in a controlled viral challenge. Holstein-Friesian calves were either inoculated with BRSV (103.5 TCID50/ml x 15 ml) (n=12) or mock challenged with phosphate buffered saline (n=6). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

18 Samples

Download data: TXT

(Submitter supplied) Gene regulation is critical for proper cellular function. Next-generation sequencing technology has revealed the presence of regulatory networks that regulate gene expression and essential cellular functions. Studies investigating the epigenome have begun to uncover the complex mechanisms regulating transcription. Assay for transposase-accessible chromatin by sequencing (ATAC-seq) is quickly becoming the assay of choice for epigenomic investigations. more...

Organism:

Drosophila melanogaster

Type:

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

Platform:

GPL17275

12 Samples

Download data: BW, CSV, HTML, NARROWPEAK, TXT, XLSX

(Submitter supplied) ATAC sequencing of bovine oocytes and early embryos revealed a genome-wide map of accessible chromatin of bovine early embryo development, highlighting the critical features of chromatin landscape and epigenetic reprogramming during bovine preimplantation embryo development.

Organism:

Bos taurus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24230

56 Samples

Download data: TXT

(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) Comprehensive analyses of tissues at single-cell level will benefit our understanding of genetic bases for complex traits. Here we present an initial effort of single-cell transcriptomic analyses of cattle ruminal epithelial cells during the rumen development. We obtained 5064 and 1372 cells from Holstein ruminal epithelial cells before and after weaning, respectively. We reported 6 cell types across their temporal and spatial distributions, which were partially correlated with rumen epithelium layer’s structures and functions. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23295

2 Samples

Download data: MTX, TSV

(Submitter supplied) Comprehensive analyses of tissues at the single-cell level will benefit our understanding of genetic bases for complex traits. We performed single-cell RNA sequencing (scRNA-seq) analyses of peripheral blood mononuclear cells (PBMCs) from Holstein cattle, investigating their cell types and responses to lipopolysaccharide (LPS) treatment in vitro. The responses to LPS treatment include innate immunity activation of monocytes, macrophages, and dendritic cells, as well as B cell proliferation. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

4 Samples

Download data: MTX, TSV

(Submitter supplied) Genome-wide methods for examining chromatin modification provide detailed information on regulatory regions of the genome.  Dynamic modifications of chromatin allow rapid access of the gene regulatory machinery to condensed genomic regions facilitating subsequent gene expression.  Inflammatory cytokine stimulation of cells can cause rapid gene expression changes through direct signalling pathway-mediated transcription factor activation and regulatory element binding.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

6 Samples

Download data: TXT

(Submitter supplied) Genome-wide methods for examining chromatin modification provide detailed information on regulatory regions of the genome.  Dynamic modifications of chromatin allow rapid access of the gene regulatory machinery to condensed genomic regions facilitating subsequent gene expression.  Inflammatory cytokine stimulation of cells can cause rapid gene expression changes through direct signalling pathway-mediated transcription factor activation and regulatory element binding.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: BW

(Submitter supplied) Twelve clinically healthy backgrounded cattle (n=6 vaccinated, n=6 non-vaccinated), over four time points (median age in days: 107, 114, 183, 230) were selected for whole blood (Tempus Blood RNA Tubes) mRNA sequencing via NovaSeq 6000 S4 workflow. Sequenced raw reads (~35M/sample) were analyzed for the influence of time (immunological development) and vaccination with a commercial modified live viral multivalent vaccine on host gene expression.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

48 Samples

Download data: TXT

(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) 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) ATAC-seq analysis of Candida albicans SC5314 treated or not treated with hydrogen peroxide to assess the accessible chromatin landscape upon oxidative stress in comparison to normal growth in YPD at 30 °C.

Organism:

Candida albicans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27827

8 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL21273 GPL28457 GPL21493

19 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) We benchmark Illumina’s HiseqX10 instrument against Beijing Genomics Institute’s (BGI) DNBSEQ-G400 platform, a considerably cheaper sequencing alternative. For comparisons, the same bulk ATAC-seq libraries generated from pluripotent stem cells (PSCs) and fibroblasts were sequenced on both platforms. Both instruments generate sequencing reads with comparable mapping rates and genomic context. However DNBSEQ-G400 data contained a significantly higher number of small, sub-nucleosomal reads (>30% increase) and a reduced number of bi-nucleosomal reads (>75% decrease), which resulted in narrower peak-bases and improved peak calling, enabling the identification of 4% more differentially accessible regions between PSCs and fibroblasts. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL28457 GPL21273

12 Samples

Download data: BW, GTF, NARROWPEAK, TXT

(Submitter supplied) We benchmark Illumina’s HiseqX10 instrument against Beijing Genomics Institute’s (BGI) DNBSEQ-G400 platform, a considerably cheaper sequencing alternative. For comparisons, the same bulk ATAC-seq libraries generated from pluripotent stem cells (PSCs) and fibroblasts were sequenced on both platforms. Both instruments generate sequencing reads with comparable mapping rates and genomic context. However DNBSEQ-G400 data contained a significantly higher number of small, sub-nucleosomal reads (>30% increase) and a reduced number of bi-nucleosomal reads (>75% decrease), which resulted in narrower peak-bases and improved peak calling, enabling the identification of 4% more differentially accessible regions between PSCs and fibroblasts. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

7 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20301 GPL20795

84 Samples

Download data

(Submitter supplied) ATAC-seq and RNA-seq of primary human neutrophils challenged with multiple pathogen mimicking ligands and whole organisms.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: TXT