{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Steve Potter"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-41993"],"description":["Hox genes are key regulators of development. In mammals, the study of these genes is greatly confounded by their large number, overlapping functions, and their interspersed shared enhancers. In this report, we describe a novel recombineering strategy that was used to introduce simultaneous frameshift mutations into the flanking Hoxa9, Hoxa10, and Hoxa11 genes, as well as their paralogs on the HoxD cluster. The resulting mutant mice displayed dramatic homeotic transformations of the reproductive tracts, with uterus anteriorized towards oviduct and the vas deferens anteriorized towards epididymis. The Hoxa9,10,11 mutant mice provided a sensitized genetic background that allowed the discovery of Hoxd9,10,11 reproductive tract patterning function. Both shared and distinct Hox functions were defined. The HoxD genes played a crucial role in the regulation of the uterine immune function. Non-coding nonpolyadenylated RNAs were among the key Hox targets. In addition, we observed a surprising anti-dogmatic posteriorization of the uterine epithelium. Reproductive tracts were collected from WT and Hox mutant mice (n=3/genotype) aged 3-7 months in order to characterize the molecular changes caused by mutation of Hoxa9,10,11 and Hoxd9,10,11. Female mice were staged and collected in diestrus."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Labeling - For each sample, the Ambion® WT Expression Kit (Life Technologies) synthesizes cDNA target from 300 nanograms of total RNA. Then the GeneChip® WT Terminal Labeling Kit (Affymetrix) is used to both chemically fragment and biotin-label the cDNA target.","Nucleic Acid Extraction - Total RNA was extracted from fresh tissue using the Qiagen RNeasy Mini kit.","Scaning - The arrays are scanned with the Affymetrix GeneChip Scanner 3000 7G following manufacturer's instructions. Raw data files are created by Command Console, the Affymetrix operating software program.","Hybridization - A hybridization cocktail is created for each sample. The samples are hybridized to a standard Probe Array Cartridge (GeneChip Mouse Gene 1.0 ST Array-Affymetrix) in the GeneChip Hybridization Oven 640 (Affymetrix). Probe arrays are washed and stained using the Fluidics Station 450 (Affymetrix)."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Data Transformation - Data were analyzed using GeneSpring GX software with the RMA16 summarization algorithm without baseline transformation. Probe sets were filtered on expression keeping only those with >150 raw expression in 1 genotype per comparison. Each Hox mutant (n=3/tissue/genotype) was compared to WT (n=3), and probe sets changed >2 fold with p<0.05 were counted as significant changes. ID_REF =  VALUE = Log2 RMA16 signal"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["Hox genes are key regulators of development. In mammals, the study of these genes is greatly confounded by their large number, overlapping functions and interspersed shared enhancers. Here, we describe the use of a novel recombineering strategy to introduce simultaneous frameshift mutations into the flanking Hoxa9, Hoxa10 and Hoxa11 genes, as well as their paralogs on the HoxD cluster. The resulting Hoxa9,10,11 mutant mice displayed dramatic synergistic homeotic transformations of the reproductive tracts, with the uterus anteriorized towards oviduct and the vas deferens anteriorized towards epididymis. The Hoxa9,10,11 mutant mice also provided a genetic setting that allowed the discovery of Hoxd9,10,11 redundant reproductive tract patterning function. Both shared and distinct Hox functions were defined. Hoxd9,10,11 play a crucial role in the regulation of uterine immune function. Non-coding non-polyadenylated RNAs were among the key Hox targets, with dramatic downregulation in mutants. We observed Hox cross-regulation of transcription and splicing. In addition, we observed a surprising anti-dogmatic apparent posteriorization of the uterine epithelium. In caudal regions of the uterus, the normal simple columnar epithelium flanking the lumen was replaced by a pseudostratified transitional epithelium, normally found near the more posterior cervix. These results identify novel molecular functions of Hox genes in the development of the male and female reproductive tracts."],"study_type":["transcription profiling by array"],"species":["Mus musculus"],"pubmed_title":["Recombineering-based dissection of flanking and paralogous Hox gene functions in mouse reproductive tracts."],"pubmed_authors":["Sara Meyer","Anna Raines","Sudhansu Dey","Bliss Magella","S Potter","Steve Potter","Raines AM, Adam M, Magella B, Meyer SE, Grimes HL, Dey SK, Potter SS","Mike Adam","H Grimes"],"additional_accession":[]},"is_claimable":false,"name":"Expression data from the reproductive tracts of WT, Hoxa9,10,11, and Hoxd9,10,11 mutant mice","description":"Hox genes are key regulators of development. In mammals, the study of these genes is greatly confounded by their large number, overlapping functions, and their interspersed shared enhancers. In this report, we describe a novel recombineering strategy that was used to introduce simultaneous frameshift mutations into the flanking Hoxa9, Hoxa10, and Hoxa11 genes, as well as their paralogs on the HoxD cluster. The resulting mutant mice displayed dramatic homeotic transformations of the reproductive tracts, with uterus anteriorized towards oviduct and the vas deferens anteriorized towards epididymis. The Hoxa9,10,11 mutant mice provided a sensitized genetic background that allowed the discovery of Hoxd9,10,11 reproductive tract patterning function. Both shared and distinct Hox functions were defined. The HoxD genes played a crucial role in the regulation of the uterine immune function. Non-coding nonpolyadenylated RNAs were among the key Hox targets. In addition, we observed a surprising anti-dogmatic posteriorization of the uterine epithelium. Reproductive tracts were collected from WT and Hox mutant mice (n=3/genotype) aged 3-7 months in order to characterize the molecular changes caused by mutation of Hoxa9,10,11 and Hoxd9,10,11. Female mice were staged and collected in diestrus.","dates":{"release":"2013-08-01T00:00:00Z","modification":"2023-09-01T09:39:41.192Z","creation":"2022-01-31T15:15:15.515Z"},"accession":"E-GEOD-41993","cross_references":{"GEO":["GSE41993"],"pubmed":["23760953"],"EFO":["EFO_0002768"],"doi":["10.1242/dev.092569"]}}