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accession-icon GSE15318
Cdcs1 a major colitis susceptibility locus in mice; subcongenic analysis reveals genetic complexity
  • organism-icon Mus musculus
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Background and Aims: In the interleukin-10-deficient (Il10-/-) mouse model of IBD, 10 quantitative trait loci (QTL) have been shown to be associated with colitis susceptibility by linkage analyses on experimental crosses of highly susceptible C3H/HeJBir (C3Bir)-Il10-/- and partially resistant C57BL/6J (B6)-Il10-/- mice. The strongest locus (C3Bir-derived cytokine deficiency-induced colitis susceptibility [Cdcs]1 on Chromosome [Chr] 3) controlled multiple colitogenic subphenotypes and contributed the vast majority to the phenotypic variance in cecum and colon. This was demonstrated by interval-specific Chr 3 congenic mice wherein defined regions of Cdcs1 from C3Bir or B6 were bred into the IL-10-deficient reciprocal background and altered the susceptible or resistant phenotype. Furthermore, this locus likely acts by inducing innate hypo- and adaptive hyperresponsiveness, associated with impaired NFB responses of macrophages. The aim of the present study was to dissect the complexity of Cdcs1 by further development and characterization of reciprocal Cdcs1 congenic strains and to identify potential candidate genes in the congenic interval. Material and Methods: In total, 15 reciprocal congenic strains were generated from Il10-/- mice of either C3H/HeJBir or C57BL/6J backgrounds by 10 cycles of backcrossing. Colitis activity was monitored by histological grading. Candidate genes were identified by fine mapping of congenic intervals, sequencing, microarray analysis and a high-throughput real-time RT-PCR approach using bone marrow-derived macrophages. Results: Within the originally identified Cdcs1-interval, three independent regions were detected that likely contain susceptibility-determining genetic factors (Cdcs1.1, Cdcs1.2, and Cdcs1.3). Combining results of candidate gene approaches revealed Fcgr1, Cnn3, Larp7, and Alpk1 as highly attractive candidate genes with polymorphisms in coding or regulatory regions and expression differences between susceptible and resistant mouse strains. Conclusions: Subcongenic analysis of the major susceptibility locus Cdcs1 on mouse chromosome 3 revealed a complex genetic structure. Candidate gene approaches revealed attractive genes within the identified regions with homologs that are located in human susceptibility regions for IBD.

Publication Title

Cdcs1 a major colitis susceptibility locus in mice; subcongenic analysis reveals genetic complexity.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE2172
IL10 deficiency
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)

Description

Abstract: Interleukin-10-deficient (Il10-/-) mice serve as a model for inflammatory bowel disease (IBD). The severity of colitis strongly depends on the inbred strain carrying the disrupted Il10 gene: C3H/HeJBir (C3) confers disease susceptibility, whereas C57BL/6J (B6) confers resistance. Genome-wide scans with microsatellite markers on segregrating backcross and F2 populations resulted in the detection of ten colitogenic quantitative trait loci (QTL). The aim of this study was to reduce the large number of candidate genes within the QTL intervals by identifying those genes which are located within the candidate gene intervals and which are differentially expressed in the colon of IBD-susceptible and -resistant strains. Using this combination of QTL mapping and microarray analysis, we identified 16 genes which were differentially expressed between B6- and C3-Il10-/- mice and were located within the candidate gene intervals. Three of these genes (Pla2g2a, Gbp1, Cd14) showed prominent differences in expression levels between B6- and C3-Il10-/- as well as between B6 and C3 wildtype mice and were considered to be major candidate genes. Pla2g2a and Gbp1 are known to be polymorphic between C3 and B6 mice. Expression data for Cd14 were confirmed by real-time RT PCR using specified pathogen free and germfree Il10-/- mice. In conclusion, the large number of candidate genes was reduced to three major candidates by using a combination of QTL mapping and microarray analysis. All three genes play an important role in inflammatory processes and immune response.

Publication Title

Cd14, Gbp1, and Pla2g2a: three major candidate genes for experimental IBD identified by combining QTL and microarray analyses.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP092744
Genes and polymorphism identification associated to hernias in swine
  • organism-icon Sus scrofa
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Transcriptome of connective tissue of swine affected and non-affected with scrotal hernia

Publication Title

No associated publication

Sample Metadata Fields

Sex, Age, Specimen part, Disease

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accession-icon GSE55570
Gene expression data of two different strains of laying hens from a small group housing system
  • organism-icon Gallus gallus
  • sample-icon 60 Downloadable Samples
  • Technology Badge Icon Affymetrix Chicken Gene 1.0 ST Array (chigene10st)

Description

We used a chicken RNA microarray to identify differentially expressed genes in order to compare two layer lines kept in a small group housing system Eurovent Deutsch.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

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accession-icon GSE38146
Effects of dietary fat types on growth performance, pork quality, and gene expression in growing-finishing pigs
  • organism-icon Sus scrofa
  • sample-icon 23 Downloadable Samples
  • Technology Badge Icon Affymetrix Porcine Genome Array (porcine)

Description

This study was performed to determine the effects of dietary fat sources, i.e., beef tallow, soybean oil, olive oil and coconut oil (each 3% in feed), on the growth performance, meat quality and gene expression in growing-finishing pigs.

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part

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accession-icon SRP194395
Eimeria maxima-Induced Transcriptional Changes in the Cecal Mucosa of the Broiler Chickens
  • organism-icon Gallus gallus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Apicomplexan protozoans of Eimeria spp. cause coccidiosis, one of the most economically relevant parasitic diseases in chickens. The lack of a complete understanding of molecular mechanisms in host-parasite interaction limits the development of effective control measures. In the present study, RNA sequencing (RNA-seq) was applied to investigate the host mRNA profiles of the cecal mucosa and its contents collected at day 5 post Eimeria maxima (EM) infection.

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part, Cell line

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accession-icon SRP149598
Cardiac gene expression in two broiler lines at two different time points
  • organism-icon Gallus gallus
  • sample-icon 20 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Male broilers from two lines (n=10 per line) with different growth rate were raised at the same condition with free access to feed and drink. At day 6 and day 21, half samples of each broiler line were euthanized by cervical dislocation, and left ventricles were collected for RNA isolation. Gene expression in left ventricle was measured by RNA-seq and compared between different time points and chicken lines. The purpose of this study is to investigate gene expression change during broiler cardiac development and to compared gene expression between fast-growing modern broilers and slow-growing heritage broilers to find possible genes and pathways related to differential cardiac development and differential susceptibility to cardiac diseases between the two broiler lines.

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part, Disease

View Samples
accession-icon SRP152925
Gallus gallus gallus Transcriptome or Gene expression
  • organism-icon Gallus gallus
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

broilers heat stress.

Publication Title

No associated publication

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon SRP081182
human fatty tissue Transcriptome
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 4000

Description

understand the funcation of fatty

Publication Title

No associated publication

Sample Metadata Fields

Sex, Age, Specimen part

View Samples
accession-icon SRP039377
The Transcriptomes of Natural Developmental Magnum in Chickens
  • organism-icon Gallus gallus
  • sample-icon 7 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

The goal of this study is to obtain the transcriptomes of chicken magnum in different natural developmental stages. There are totally five stages researched in this study and they are named D1, D2, D3, D4 and L. D1 to D4 are the abbreviations of developmental stage 1 to developmental stage 4 and L means laying stage. D1 refers to the lag phase (about 7 weeks old) in which the magnum has very slight change; D2 refers to the early proliferation phase (about 13 weeks old); D3 refers to the late proliferation phase (about 16 weeks old); D4 refers to the early differentiation phase (about 17 weeks old).

Publication Title

No associated publication

Sample Metadata Fields

Age

View Samples
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refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

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Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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