GEO DataSets

(Submitter supplied) Using the distribution of Influenza-infected phenotypes (immunohistochemical (IHC) staining for viral protein and weight loss at 4 days post infection) in 99 Influenza-infected pre-Collaborative Cross (CC) lines, we have categorized the extreme phenotypes with regard to host response: severe (“high”) response to infection (N=26, IHC score: 4 or 5, % Weight loss > 15%) and mild (“low”) response to infection (N=18, IHC score: 0 or 1, % Weight loss < 5%). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

44 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11202

93 Samples

Download data: TXT

(Submitter supplied) To determine if genetic background can modulate severity of an infection, we studied the host responses to influenza infections in the eight genetically highly diverse Collaborative Cross (CC) founder mice.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11202

43 Samples

Download data: TXT

(Submitter supplied) To determine if genetic background can modulate severity of an infection, we studied the host responses to influenza infections in the eight genetically highly diverse Collaborative Cross (CC) founder mice.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11202

50 Samples

Download data: TXT

(Submitter supplied) We aimed at systematically inferring the regulatory functions of host lncRNAs in response to influenza A virus (IAV) and severe acute respiratory syndrome coronavirus (SARS-CoV) in the mouse model, using a ‘guilt-by-association’ approach which relies on finding which lncRNAs have similar expression profiles to protein-coding genes of known function. To build a large panel of diverse host responses to viral infection, we took advantage of the genetic diversity present in the 8 founder strains of the Collaborative Cross (CC) mouse resource. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11002

123 Samples

Download data: TXT

(Submitter supplied) The goal of this project was to identify strain-dependent expression of miRNAs in lung tissue from Collaborative Cross founder strains that were sensitized and challenged with house dust mite allergen (Der p 1).

Organism:

synthetic construct; Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL14613

32 Samples

Download data: CEL

(Submitter supplied) Seasonal influenza outbreaks and recurrent influenza pandemics present major challenges to public health. By studying immunological responses to influenza in different host species, it may be possible to discover common mechanisms of susceptibility in response to various influenza strains. This could lead to novel therapeutic targets with wide clinical application. Using a mouse-adapted strain of influenza (A/HK/1/68-MA20 [H3N2]), we produced a mouse model of severe influenza (p-flu) that reproduces the hallmark high viral load and overexpression of cytokines associated with susceptibility to p-flu in humans. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL81

54 Samples

Download data: CEL

(Submitter supplied) Susceptible and Resistant mouse strain, e.g. DBA/2J and C57BL/6J respectively, were inoculated with a highly pathogenic H5N1 influenza A virus (A/Hong Kong/213/2003) for 72 hours. Differences in expression were analyzed and use to identify candidate genes and pathways that contributed to the difference in H5N1 pathogenesis in these two strains. Recombinant inbred BXD strains are derived from the DBA/2J and C57BL/6 parent and were used to identify genetic loci associated with resistant to H5N1 infection.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

37 Samples

Download data: CEL, TXT

(Submitter supplied) In this study, we performed a cross-species gene expression study of the peripheral blood from the Collaborative Cross (CC) mouse population after Influenza virus (IV).

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11202

127 Samples

Download data: TXT

(Submitter supplied) The host response to influenza A infections is strongly influenced by host genetic factors. Animal models of genetically diverse mouse strains are well suitable to identify host genes involved in severe pathology, viral replication and immune responses. Here, we have utilizing a dual RNAseq approach that allowed us to investigate both viral and host gene expression in the same individual from a single expression assay after H1N1 infection. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16790

36 Samples

Download data: TXT

(Submitter supplied) The Collaborative Cross (CC) recombinant inbred panel was conceived as an ideal resource for mammalian system genetics. The pre-CC is a proof-of-concept experiment involving CC lines that have undergone at least five generations of inbreeding. Siblings from these lines were each involved in one of four distinct phenotyping arms, then genotyped on a high-density Affymetrix platform. The genetic profile of these emerging lines reveals high diversity, balanced allele frequencies, and well-distributed recombination – all ideal qualities for a mapping panel. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10528

157 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL8833

104 Samples

Download data

(Submitter supplied) Susceptible (DBA/2J, 129/SvImJ, A/J) and Resistant (SM/J, C57BL/6J, Balb/cJ) mouse strain were inoculated with a highly pathogenic H5N1 influenza A virus (A/Hong Kong/213/2003) for 72 hours or not infected (control animals). Differences in expression were analyzed and used to identify candidate genes and pathways that contributed to the difference in H5N1 pathogenesis in these two groups of mice.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL8833

35 Samples

Download data: TXT

(Submitter supplied) Susceptible (DBA/2J, 129/SvImJ, A/J) and Resistant (SM/J, C57BL/6J, Balb/cJ) mouse strain were inoculated with a highly pathogenic H5N1 influenza A virus (A/Hong Kong/213/2003) for 24 and 168 hours. Uninfected control animals were included. Differences in expression were analyzed and used to identify candidate genes and pathways that contributed to the difference in H5N1 pathogenesis in these two groups of mice.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL8833

69 Samples

Download data: TXT

(Submitter supplied) To determine the transcriptional response to Salmonella enterica serovar Enteritidis (SE) infection, a newly developed chicken 44K Agilent array was used to analyze total RNA of heterophils from SE-resistant (line A) and SE–susceptible chickens (line B), treated with in vitro infection of SE (I) or non SE medium (N) for 1 hr. A dual-color balanced design was used to provide a direct comparison between SE-infected and non-infected groups (AI/AN, BI/BN) and between line A and line B (AN/BN, AI/BI). more...

Organism:

Gallus gallus

Type:

Expression profiling by array

Platform:

GPL4993

16 Samples

Download data: GPR

(Submitter supplied) While genetic variants are known to be associated with overall gene abundance in stimulated immune cells, less is known about their effects on alternative isoform usage. Analyzing RNA-seq profiles of monocyte-derived dendritic cells from 243 individuals, we uncovered thousands of unannotated isoforms synthesized in response to influenza infection and type 1 interferon stimulation. We identified more than a thousand quantitative trait loci (QTLs) associated with alternate isoform usage (isoQTLs), many of which are independent of expression QTLs for the same gene. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

576 Samples

Download data: BED, TXT

(Submitter supplied) A central challenge in pharmaceutical research is to investigate genetic variation in response to drugs. The Collaborative Cross (CC) mouse reference population is a promising model for pharmacogenomic studies because of its large amount of genetic variation, genetic reproducibility, and dense recombination sites. While the CC lines are phenotypically diverse, their genetic diversity in drug disposition processes, such as detoxification reactions, is still largely uncharacterized. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

55 Samples

Download data: TXT

(Submitter supplied) BACKGROUND: The genetics of transcript-level variation is an exciting field that has recently given rise to many studies. Genetical genomics studies have mainly focused on cell lines, blood cells or adipose tissues, from human clinical samples or mice inbred lines. Few eQTL studies have focused on animal tissues sampled from outbred populations to reflect natural genetic variation of gene expression levels in animals. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL3729

57 Samples

Download data: TXT

(Submitter supplied) Background: The 2009 pandemic H1N1 influenza virus emerged in swine and quickly became a major global health threat. In mouse, non-human primate, and swine infection models, the pH1N1 virus efficiently replicates in the lung and induces pro-inflammatory host responses; however, whether similar or different cellular pathways were impacted by pH1N1 virus across independent infection models remains to be further defined. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL10162

9 Samples

Download data: TXT

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

Organism:

Mus musculus; Macaca mulatta; Sus scrofa; Macaca fascicularis

Type:

Expression profiling by array

Platforms:

GPL7202 GPL10162 GPL14569

79 Samples

Download data: TXT