Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Estrogen and mTORC1 dependent genes in the uterus of uterine-specific Tsc2-null mice

ABSTRACT: To uncover genes regulated by mTORC1 and estradiol in uterine Tsc2-null LAM like cells, we performed RNAseq on uteri from 12-week old wild-type (WT) and uterine-specific Tsc2-null (KO) mice that were either untreated (intact), oopherectomized (ovx) or oopherectomized + treated with 17Î²-estradiol pellets (E2) for 8 weeks. We identified genes that were both estradiol- and TSC2-mediated. Uterine mRNA profiles of 12 week old wild type (WT) and uterine-specific Tsc2-null (KO) mice in the presence or absence of estradiol were generated using Illumina HiSeq2500

ORGANISM(S): Mus musculus

SUBMITTER: Stephen Hammes

PROVIDER: E-GEOD-78701 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Estrogen maintains myometrial tumors in a lymphangioleiomyomatosis model.

Prizant Hen H Taya Manisha M Lerman Irina I Light Allison A Sen Aritro A Mitra Soumya S Foster Thomas H TH Hammes Stephen R SR

Endocrine-related cancer 20160215 4

Lymphangioleiomyomatosis (LAM) is a rare disease in women. Patients with LAM develop metastatic smooth-muscle cell adenomas within the lungs, resulting in reduced pulmonary function. LAM cells contain mutations in tuberous sclerosis genes (TSC1 or TSC2), leading to up-regulation of mTORC1 activity and elevated proliferation. The origin of LAM cells remains unknown; however, inactivation of Tsc2 gene in the mouse uterus resulted in myometrial tumors exhibiting LAM features, and approximately 50% ...[more]

PMID: 26880751

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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study were to compare signals from competent and abnormal human embryos impacted differently on the expression of endometrial receptivity genes in mouse uteri using transcriptome profiling (RNA-seq). Methods: Immature female (25 d C57BL/6) mice were given a hormone treatment of a single dose 1 mg progesterone and 10 mg/kg/day ÃÂ²-estradiol for a total of 3d to prime the uterus for embryo transfer. The uterine horns of control and study mice were injected with an equal volume (50 ÃÂ¼l) of either unconditioned embryo culture medium (ECM), serving as controls, or pooled conditioned media from competent (n = 9) or arresting embryos (n = 18). Uterine mRNA profiles of 25-day-old wild-type (WT) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000 platform. The sequence reads that passed quality filters were analyzed with the following methods: Bowtie Alignment followed by TopHat (splice juntions mapper) and Cufflinks (transcript abundance). qRTÃ¢ÂÂPCR validation was performed using SYBR Green assays. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the uteri WT and NrlÃ¢ÂÂ/Ã¢ÂÂ mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRTÃ¢ÂÂPCR. RNA-seq data had a linear relationship with qRTÃ¢ÂÂPCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and NrlÃ¢ÂÂ/Ã¢ÂÂ retina, with a fold change Ã¢ÂÂ¥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRTÃ¢ÂÂPCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study represents the first detailed analysis of maternal uterine reponse to signals from competent and abnormal human embryos, with biological replicates, generated by RNA-seq technology. Supernatant from competent and abnormal human embryos were flushed into the uterine horns of 25d old C57BL/6 female mice. Uterine mRNA profiles of 21-day old mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000 platform (HiSeq).

Dataset Information

Estrogen and mTORC1 dependent genes in the uterus of uterine-specific Tsc2-null mice

Publications

Estrogen maintains myometrial tumors in a lymphangioleiomyomatosis model.

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