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Mus musculus
24 Downloadable Samples
Illumina HiSeq 2500
Description
Despite decades of interest, the mechanisms that control Hox gene expression are not yet fully understood. It was recently proposed that Hotair, a lncRNA transcribed from the HoxC cluster, regulates HoxD gene expression via Polycomb targeting and thus is important for correct skeletal development. However, genetic manipulations of the locus led to conflicting results regarding the roles of Hotair. Here, we analyze the molecular and phenotypic consequences of deleting the Hotair locus in vivo. In contradiction with previous findings, we show that deleting Hotair has no detectable effect on HoxD gene expression in vivo. We could not observe any morphological alteration in mice lacking the Hotair locus. However, we find a significant impact of deleting Hotair on the expression of neighboring genes Hoxc11 and Hoxc12. Our results do not support an RNA-dependent role for Hotair in vivo, but argue in favor of a DNA-dependent effect of Hotair deletion on the transcriptional landscape in cis. Overall design: We micro-dissected wild type and Del(Hotair)-/- E12.5 embryos into 6 segments: forelimbs (FL), hindlimbs (HL), genital tubercle (GT), trunk section corresponding to the lumbar/sacral region (T1); trunk section corresponding to the sacral/caudal region (T2) and trunk section corresponding to the caudal region (T3). We generated strand-specific RNA-seq data for each segment, in two biological replicates and we performed differential expression analyses for each tissue. Furthermore, we analyzed the impact of deleting the Hotair locus on the local transcriptional landscape, in the HoxC cluster.
Publication Title
Hotair Is Dispensible for Mouse Development.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
Hox genes are required for the development of the intestinal caecum, a major organ of species eating plants. We have analysed the transcriptional regulation of Hoxd genes in caecal buds and show that they are controlled by a series of enhancers located in a gene desert telomeric to the HoxD cluster. The start site of two neighboring and opposite long non-coding RNAs, Hotdog and Twin of Hotdog, specifically transcribed in the caecum, contacts the expressed Hoxd genes in the framework of a topological domain, a large domain of interactions, which ensures a robust transcription of these genes during caecum budding. We show that hedgehogs have kept this regulatory potential despite the absence of caecum, suggesting that these enhancers are used in other developmental situations. In this context, we discuss some striking similarities between the caecum and the limb buds, suggesting the implementation of a common budding tool-kit. Overall design: Transcriptional activity at the HoxD locus in the murine developing gut at E13, Differential gene expression analysis along the murine developing gut
Publication Title
Multiple enhancers regulate Hoxd genes and the Hotdog LncRNA during cecum budding.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples
SRP018708- Mus musculus
- 1 Downloadable Sample
- Illumina Genome Analyzer II
Description
Hox genes are required for the development of the intestinal caecum, a major organ of species eating plants. We have analysed the transcriptional regulation of Hoxd genes in caecal buds and show that they are controlled by a series of enhancers located in a gene desert telomeric to the HoxD cluster. The start site of two neighboring and opposite long non-coding RNAs, Hotdog and Twin of Hotdog, specifically transcribed in the caecum, contacts the expressed Hoxd genes in the framework of a topological domain, a large domain of interactions, which ensures a robust transcription of these genes during caecum budding. We show that hedgehogs have kept this regulatory potential despite the absence of caecum, suggesting that these enhancers are used in other developmental situations. In this context, we discuss some striking similarities between the caecum and the limb buds, suggesting the implementation of a common budding tool-kit. Transcriptional activity at the HoxD locus in developing caeca at E13.5 Overall design: Transcriptional activity at the HoxD locus in developing caeca at E13.5
Publication Title
Multiple enhancers regulate Hoxd genes and the Hotdog LncRNA during cecum budding.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 1 Downloadable Sample
- Illumina HiSeq 2500
Description
Analysis of gene expression in the distal forelimbs Overall design: RNA-Seq polyA on transcripts extracted from the dissection of three pairs of embryonnic forelimbs at E12.5
Publication Title
Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states.
Sample Metadata Fields
Cell line, Subject
View Samples GSE1867- Mus musculus
- 14 Downloadable Samples
Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
To elucidate biological processes underlying the keratocyte, fibroblast, and myofibroblast phenotypes of corneal stromal cells, the gene expression patterns of these primary cultures from mouse cornea were compared with those of the adult and 10-day postnatal mouse cornea.
Publication Title
Microarray studies reveal macrophage-like function of stromal keratocytes in the cornea.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 7 Downloadable Samples
- Illumina HiSeq 2500
Description
To study mechanisms of long bone growth regulation, p21 misexpression was induced in the left hindlimb of mouse embryos using an intersectional approach that requires both Cre and (r)tTA activity. Doxycycline was provided to the pregnant female at embryonic day (E)12.5 to activate the transgene, and embryos were collected at E17.5. Distal femur and proximal tibia growth plates were dissected out, keeping left and right separated, deprived of perichondrium and flash frozen. After RNA extraction, mRNA libraries were prepared and all samples were deep sequenced in parallel Overall design: 6 samples (left and right growth plates from embryos #386, #387, #388) were sequenced in parallel
Publication Title
Cell-nonautonomous local and systemic responses to cell arrest enable long-bone catch-up growth in developing mice.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 18 Downloadable Samples
- Illumina HiSeq 2500
Description
We report the application of RNA-sequencing for high-throughput profiling of gene expression in hedgehog-responsive stromal cells in normal mouse prostate and mouse prostate tumors. By using the Gli1-GFP knock-in reporter mouse line, we isolated the subset of mouse prostate stromal cells undergoing hedgehog signaling to compare the transcriptomes between PB-MYC prostate tumor and normal prostate in mice at the age of about 45 weeks. Overall design: The mRNA profiles of hedgehog-responsive stromal cells in 45-week old wild type (WT) prostates and PB-MYC prostate tumors were generated by RNA-sequencing, in triplicate, using Illumina HiSeq 2000.
Publication Title
Stromal hedgehog signaling maintains smooth muscle and hampers micro-invasive prostate cancer.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
Acute viral infection typically generates functional effector CD8+ T cells that aid in pathogen clearance. However, during acute viral lower respiratory infection (LRI), lung CD8+ T cells are functionally impaired and do not optimally control viral replication, while spleen CD8+ T cells specific for the same viral epitopes remain fully functional. To better understand the mechanisms governing lung CD8+ T cell impairment, we used flow cytometry to sort anti-viral CD8+ T cells during viral LRI. Lung and spleen cells were stained with MHC-class I tetramers representing the immunodominant anti-viral CD8+ T cell epitope. We then sorted to high purity: nave CD8+ T cells, spleen epitope-specific CD8+ T cells, lung epitope-specific CD8+ cells and secondary infection lung epitope-specific CD8+ T cells. We then performed a genome wide transcriptional analysis of these cells to characterize the gene expression profile of lung CD8+ T cell impairment.
Publication Title
Acute Viral Respiratory Infection Rapidly Induces a CD8+ T Cell Exhaustion-like Phenotype.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 66 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
We report the application of Illumina small RNA sequencing to normal human skin, as well as uninvolved and involved psoriatic skin. By obtaining over 600 million qualified reads from 20 healthy controls and 47 psoriasis biopsies (uninvolved/involved), we have generated a complete small RNA profile in normal and diseased human skin, with particular emphasis on miRNAs. We report the discovery of 284 putative novel miRNAs as well as 98 differentially expressed miRNAs in psoriatic skin. Overall design: miRNA discovery and expression profiling in 67 normal and psoriatic human skin biopsies
Publication Title
Deep sequencing of small RNAs from human skin reveals major alterations in the psoriasis miRNAome.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Subject
View Samples- Ovis aries
- 40 Downloadable Samples
- Ovine Gene 1.1 ST Array (ovigene11st)
Description
Feeding animals with either concentrates supplemented with vitamin E or alfalfa grazing has been proven to reduce the oxidative process that occurs in meat products. Indoor-kept lambs were fed a standard concentrate (n=7, C) or concentrate supplemented with vitamin E (n=7, VE) for 30 days before slaughtering all animals at 2224 kg of live weight. Simultaneously, 7 unweaned lambs grazed in alfalfa paddocks (ALF) with their dams. Global transcriptomic data of longissimus thoracis (LT) muscle and subcutaneous fat (SF) with the Affymetrix Ovine Gene 1.1 microarray was used. In LT muscle when ALF group was compared with C group, were identified 41 genes differentially expressed. Among these genes 32 were down- regulated and 9 were up- regulated. Meanwhile when VE treatment was compared with C group were identified a total of 29 genes, 26 were down- regulated and 3 genes were up- regulated. In SF when ALF treatment was compared with C, were identified only 4 genes differentially expressed, all of them up-regulated in ALF group. Meanwhile when VE treatment was compared with C group, were identified a total of 330 genes. Among them, 295 genes were up- regulated and 35 were down- regulated. In LT muscle the clusters corresponding to gene expression profiles from treatments ALF, C and VE were clearly separated from each other. In SF, ALF group, overlap with VE and C treatments, however, VE and C clearly were separate in different clusters. These differentially expressed genes were selected for a functional analysis by using DAVID. In LT muscle some of the identified significant biological processes were catabolic and lipid process (down-regulated, except CPT1B) (CPT1B, PLA2G16, SPSB1, LRTOMT, PLCD4, FBXO9, CNBP and CYP27A1) and muscle organ differentiation (down-regulated) (CPT1B, MYOD1, MYLK2 and MSTN) in ALF; whereas intracellular signaling cascade (IGF1R, DEF8, AKAP7 and CISH) was down-regulated. In SF, vitamin E supplementation had an important effect; most of the genes were up-regulated. DAVID analysis showed that biosynthesis lipid pathway was the most represented with 20 genes, such as EBP, MVD, CYP51A1, DHCR7, HMGCS1, LSS and FDFT1 implicated in cholesterol synthesis. Further exploration of the links between these genes and vitamin E will lead to a better understanding of how vitamin E affects the oxidative process that occurs in meat products.
Publication Title
Genome-wide expression profiling in muscle and subcutaneous fat of lambs in response to the intake of concentrate supplemented with vitamin E.
Sample Metadata Fields
Sex, Treatment
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