GEO DataSets

(Submitter supplied) The domestic pig (Sus scrofa) provides a large animal model for human innate immune responses and inflammation that is also economically important in its own right. Results: We demonstrate that macrophages can be harvested from 3 different compartments of the pig (lungs, blood and bone-marrow), cryopreserved and subsequently recovered and differentiated in CSF-1. We have performed surface marker analysis and gene expression profiling on macrophages from these compartments, comparing 25 animals from 5 different breeds and their response to lipopolysaccharide. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL16569

140 Samples

Download data: CEL

(Submitter supplied) Mouse bone marrow-derived macrophages (BMDM) grown in macrophage colony-stimulating factor (CSF-1) have been used widely in studies of macrophage biology and the response to toll-like receptor agonists. We investigated whether similar cells could be derived from the domestic pig. Cultivation of pig bone marrow cells for 5-7 days in presence of rhCSF-1 generated a pure population of BMDM that expressed the usual macrophage markers (CD14, CD16, CD163, CD172a), are potent phagocytic cells and produced tumor necrosis factor (TNF) in response to lipopolysaccharide (LPS). more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL3533

23 Samples

Download data: CEL

(Submitter supplied) Background: During the past 25 years, selection of production traits highly increased pig production but diseases have emerged that may cause economic loss of extreme importance. Designing sustainable animal production that better balances productivity with resistance to disease is a major concern and challenge for the next decade. In order to address questions related to immunity and resistance to disease, it is necessary to increase knowledge on the pig immune system and to produce efficient tools dedicated to this species. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL7151

28 Samples

Download data: GPR

(Submitter supplied) Differentiation of myeloid progenitor cells leads to distinct populations of mononuclear phagocytes.Various macrophages exhibit distinct biological properties. Here wanted to delineate and characterize gene expression patterns in bone marrow derived macrophages Here wanted to delineate and characterize gene expression patterns in two newly established, self-renewing, in vitro grown non-transformed lines (MPI cells) and in the SP37A3 immature myeloid dendritic cell line. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

12 Samples

Download data: CEL

(Submitter supplied) Rationale: Lipopolysaccharide (LPS) is ubiquitous in the environment. Inhalation of LPS has been implicated in the pathogenesis and/or severity of several lung diseases, including pneumonia, chronic obstructive pulmonary disease and asthma. Alveolar macrophages are the main resident leukocytes exposed to inhaled antigens. Objectives: To obtain insight into which innate immune pathways become activated within human alveolar macrophages upon exposure to LPS in vivo.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4419

Platform:

GPL570

14 Samples

Download data: CEL

Analysis of alveolar macrophages purified from bilateral bronchoalveolar lavage after saline instillation into a lung segment followed by LPS instillation into the contralateral lung. Results provide insight into innate immune pathways activated in alveolar macrophages exposed to LPS in vivo.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 7 individual, 2 stress sets

Platform:

GPL570

Series:

GSE40885

14 Samples

Download data: CEL

(Submitter supplied) Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask what are the relative contributions of breed or sex when assessed across tissues. Are all tissues equally affected by breed or sex? How relevant is tissue in terms of total transcriptome variability? Keywords: breeds, sex and tissues comparison

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL3533

64 Samples

Download data: CEL

(Submitter supplied) Human alveolar macrophages (HAM) are primary bacterial niche and immune response cells during Mycobacterium tuberculosis (M.tb) infection, and human blood monocyte-derived macrophages (MDM) are a model for investigating M.tb-macrophage interactions. Here, we use a targeted RNA-Seq method to measure transcriptome-wide changes in RNA expression patterns of freshly obtained HAM (used within 6 h) and 6 day cultured MDM upon M.tb infection over time (2, 24 and 72 h), in both uninfected and infected cells from three donors each. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL17303

36 Samples

Download data: TXT

(Submitter supplied) Porcine reproductive and respiratory syndrome caused by porcine reproductive and respiratory syndrome virus (PRRSV) is an infectious disease characterized by severe reproductive deficiency in pregnant sows, respiratory symptoms in piglets, and high mortality. In this study, we employed Affymetrix microarray chip technology to compare the gene expression profiles of lung tissue samples from Dapulian (DPL) pigs (a Chinese indigenous pig breed) and Duroc×Landrace×Yorkshire (DLY) pigs after infection with PRRSV. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL3533

6 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) Background Among transcriptomic studies, those comparing species or populations can increase our understanding of the impact of the evolutionary forces on the differentiation of populations. A particular situation is the one of short evolution time with breeds of a domesticated species that underwent strong selective pressures. In this study, the gene expression diversity across five pig breeds has been explored in muscle. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL18437

147 Samples

Download data: TXT

(Submitter supplied) Bacillus anthracis is a gram-positive, aerobic, spore-forming, rod-shaped bacterium which has recently been used as an agent of bioterrorism. Because there is a significant delay between the initial contact of the spore with the host and clinical evidence of disease, there appears to be temporary containment of the pathogen by the innate immune system. Contact with the human alveolar macrophage (HAM) plays a key role in the innate immune response to B. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

7 Samples

Download data: CEL

(Submitter supplied) In this study, we generated the PBMC transcriptome data of 3 Landrace, and 3 indigenous Ghurrah pigs before and 7 days after Classical Swine fever vaccination. The piglets were 8-12 weeks of age. The sequencing was done on Illumina X-Ten platform, generating average of 39 million 150 bp paired end reads for each sample.

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22918

12 Samples

Download data: TXT

(Submitter supplied) Purpose: The aim of present research was to identify miRNAs potentially related with muscle growth in pig Methods: miRNA-seq analysis was performed on longissimus lumborum samples collected from 13 pigs representing two sire-line breeds – Pietrain and Hampshire. Based on dissection data, pigs were selected from a larger population in terms of weight of loin muscle to obtain the most extreme groups in each breed The miRNA libraries were constructed form total RNA with the use Neb Next Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the protocol. more...

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21186

13 Samples

Download data: FA, XLSX

(Submitter supplied) Porcine alveolar macrophages (PAMs) play impoartant role in innate immunity. Haemophilus parasuis is the etiological agent of Glasser’s disease in pigs. We used microarrays to study the transcriptome of PAMs infection with Haemophilus parasuis.

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL3533

6 Samples

Download data: CEL

(Submitter supplied) Purpose: MicroRNAs (miRNAs) are non-coding small miRNA ~22 nucleotides in length and play a vital role in muscle development by binding to messenger RNAs (mRNAs). Large White (LW, a lean type pig) and Meishan pigs (MS, a Chinese indigenous obese breed) have significant postnatal phenotype differences in growth rate, muscle mass and meat quality, and theses difference are programmed during prenatal muscle development.To shed directly light on the miRNA transcriptome difference in prenatal muscles between these two distinct pig breeds. more...

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11429

6 Samples

Download data: XLS

(Submitter supplied) Identification of PPARG regulated genes in human GM-CSF polarized monocyte-derived macrophages by siRNA knock-down approaches.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL21185

6 Samples

Download data: TXT

(Submitter supplied) Porcine alveolar macrophages (PAMs) play impoartant role in innate immunity. Porcine circovirus type 2 (PCV2) has been identified as the causal agent of postweaning multisystemic wasting syndrome, an economically important multifactorial disease of the swine industry worldwide. We used microarrays to study the transcriptome of PAMs infection with PCV2.

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL13968

6 Samples

Download data: LSR, TXT

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

Organism:

Bos taurus

Type:

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

Platform:

GPL19150

32 Samples

Download data: TXT

(Submitter supplied) We report the results of MIRA-Seq based high-throughput profiling of the bovine dermal fibroblast methylome from two different breeds of cattle (n=4/breed) to determine the breed-dependent differences in methylation.

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19150

8 Samples

Download data: TXT

(Submitter supplied) We report the breed-dependent differences in the innate immune response of dermal fibroblasts following exposure to lipopolysaccharide (LPS). Skin biopsies were collected from Angus (a beef breed) and Holstein (a dairy breed) animals and isolated fibroblasts were exposed to LPS to investigate differences in gene expression between these two cattle breeds.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19150

24 Samples

Download data: TXT