Mammary development during pregnancy (controlateral control vs. cleared fat pad) to define transdifferentiation factors
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE50447 | GEO | 2014/03/31
SECONDARY ACCESSION(S): PRJNA217504
REPOSITORIES: GEO
Similar Datasets
Project description:Tissue from cleared mammary fat pad and sham-operated controlateral control was removed before and at 10, 15,17, and 19 days of pregnancy. Cleared vs. controlateral tissue was hybridized in dye-swap design to in-house cDNA microarry platform. This design aims to identify factors signaling from the epithelial part of the mammary gland to the surrounding fat pad to initiate adipo-epithelial transdifferentiation. We surgically removed the epithelial part of the 4th mammary gland (including the nipple and the rudimentary ductal tree) in three weeks old CD1 mice where the ductal anlage is confined to the proximal part of the mammary fat pad close to the nipple. The controlateral gland was sham-operated as control. This leaves a cleared mammary fat pad in its endogenous environment. The dissected tissues were subjected to whole mount analysis to judge if the removal of epithelial tissue was complete. At the age of 10 to 15 weeks the tissues were harvested before and 10, 15, 17, and 19 days after the start of pregnancy. RNA from cleared fat pads were compared to sham-operated contralateral controls by competitive hybridization on two-channel microarrays. If enough material was available three different pools of RNA (= three biological replicates) were used for hybridization (from d19 material only two replicates were obtained) in a dye-swap configuraiton (one biological replicate of d17 and d19 samples did not provide sufficient amount for a dyw-swap pair).
2014-03-31 | E-GEOD-50447 | biostudies-arrayexpress
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2022-08-12 | PXD028953 | Pride
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2024-02-02 | GSE224418 | GEO
Project description:Gene expression from epidydimal fat pad of wild type C57BL6/J and Apoliprotein E (EKO) mice on C57BL6/J mice Whole tissue of wild type and EKO mice fed with normal and high fat diet (3 and 4 biological replicates)
2013-12-01 | E-GEOD-44653 | biostudies-arrayexpress
Project description:Mammary development during pregnancy (controlateral control vs. cleared fat pad) to define transdifferentiation factors
| PRJNA217504 | ENA
Project description:Direct transcriptomics comparison corroborated by functional and gene network analyses of pre-weaned bovine mammary parenchyma and fat pad shed light on potential cross-talk between these developing tissues. Transcriptomic characterization of mammary parenchyma and fat pad and their interaction is still incomplete. In the present experiment, the molecular epithelial-fat pad cross-talk during mammary development was assessed by transcript profiling and functional analyses. Background: Interactions between bovine mammary parenchyma (PAR) and fat pad (MFP) during neonatal tissue development are still not fully understood. It is thought that the MFP surrounding the parenchymal tissue exerts proliferative effects on the PAR through secretion of local modulators of growth induced by systemic hormones. Main objectives in the present study were to use bioinformatics tools to characterize differences in transcript profiles between mammary PAR and MFP from Holstein heifers at ca. 65 d age and uncover potential cross-talk between the two tissues via the analyses of signaling molecules (e.g., cytokines and growth factors) preferentially expressed in one tissue relative to the other. Results: Over 9,000 differentially expressed genes (DEG; False discovery rate ≤ 0.05) were found of which 1,478 had a ≥1.5-fold difference. Within these DEG in PAR vs. MFP (n = 736) we noted enrichment of functions related to cell cycle, structural organization, signaling, and DNA/RNA metabolism. Few canonical pathways were among DEG and were mostly involved in cell cycle and tissue organization (p53 signaling). Enriched among DEG more highly-expressed in MFP vs. PAR (n = 742) were genes involved in lipid metabolism, signaling, cell movement, and immune-related functions. Canonical pathways associated with metabolism (fatty acid metabolism) and signaling, particularly immune- (acute phase response) and metabolism-related (cAMP signaling), were significantly enriched. Network analysis uncovered a central role of MYC, TP53, and CTNNB1 in controlling expression of DEG highly-expressed in PAR vs. MFP. Similar analysis revealed a central role of PPARG, KLF2, EGR2, and EPAS1 in regulating expression of highly-expressed DEG in MFP vs. PAR. Analyses revealed putative crosstalk between tissues via differential expression of cytokines and growth factors highly-expressed in PAR (angiopoietin-1, osteopontin, interleukin-1β) or in MFP (adiponectin, interleukin-13, fibroblast growth factor-2, leptin) during bovine mammary development. Conclusions: We uncovered specific transcriptomic signatures characterizing MFP and PAR tissue. Not surprisingly, the expression profile of the MFP is characteristic of adipose tissue, and the one of PAR is characteristic of an epithelial tissue undergoing expansion and remodeling. Overall, our data highlighted a large degree of interaction between the two tissues and allowed envisaging a reciprocal influence in determining the biological features (and perhaps the fate) of each of the two tissues during this stage of development. This is strongly suggested by the potential effect that the signaling molecules released preferentially by PAR have on lipid metabolism-related pathways, which from our data was what most distinguished the MFP from PAR. Similarly, the cytokines and growth factors largely expressed in MFP potentially affect the pathways related to cell cycle, development, and proliferation in PAR, which our data highlighted as the main functions represented among the genes highly expressed in PAR vs. MFP. Based on the current analysis, the number of cytokines and growth factors that potentially are secreted by each tissue and affect molecules in the other underscores the concept of crosstalk. Ultimately, these bidirectional interactions might be required to coordinate mammary tissue development under normal circumstances or in response to environmental stimuli, such as nutrition.
2010-06-01 | GSE20363 | GEO
Project description:Gene expression from epidydimal fat pad of wild type C57BL6/J and Apoliprotein E (EKO) mice on C57BL6/J mice
2013-12-01 | GSE44653 | GEO
Project description:Characterizing estrogen-responsive genes is an essential step towards fully understanding mechanisms of estrogen action during mammary gland development and function. To catalogue these genes, sixteen prepubertal heifers were used in a 2 x 2 factorial with ovarian status (intact or ovariectomized) as the first factor and estrogen treatment as the second (control or estradiol). Heifers were ovariectomized at approximately 4.5 months of age and estrogen treatments were initiated one month later. After 3 days of treatment, gene expression in the parenchyma and fat pad of the bovine mammary gland was analyzed using a high-density oligonucleotide microarray. This microarray contained probes representing 40,808 Tentative Consensus sequences from the TIGR Bos taurus Gene Index and 4,575 singletons derived from libraries of pooled mammary gland and gut tissues. Microarray data were analyzed using the SAS Mixed Procedure with permutation testing. A total of 125 estrogen-responsive genes were identified using an experiment-wide permutation-based significance level of P < 0.1. Among these genes are known estrogen-targeted genes such as stanniocalcin 1, alpha-1-antiproteinase, progesterone receptor, nucleobindin 2, insulin-like growth factor 1, and tissue factor pathway inhibitor. However, the majority of the genes identified were not previously reported to be estrogen-responsive. In silico mapping and an estrogen response element (ERE) search indicated potential EREs in the promoter regions of some of these novel estrogen-responsive genes. The distinctive expression patterns regulated by estrogen in parenchyma and fat pad suggest mechanisms of action and reciprocal signaling between cell types. Keywords: Cell type comparision, two class unpaired design
2006-01-28 | GSE4054 | GEO
Project description:ChIP-seq on human omental fat pad For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2017-10-23 | GSE105689 | GEO
Project description:ATAC-seq on human mesenteric fat pad For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2021-03-30 | GSE170604 | GEO