Rattus norvegicus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA258577 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1555115_1.fastq.gz | Fastqsanger.gz | |||
| SRR1555115_2.fastq.gz | Fastqsanger.gz | |||
| SRR1555116_1.fastq.gz | Fastqsanger.gz | |||
| SRR1555116_2.fastq.gz | Fastqsanger.gz | |||
| SRR1555117_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: A novel member of RNAs, circular RNAs (circRNAs), has recently been evidenced to play key role on biological process regulation. However, the global landscape of circular RNA remains largely unknown. In the present study, deep RNA-sequencing technique was employed to identify and characterize the circular RNAs expressed in lactating rat mammary gland.compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods:Deep RNA-sequencing technique was employed Results: A total of 6824 and 4523 circRNAs were identified from rat mammary glands at two lactation stages, respectively. Numerous circRNAs seem to be specifically expressed in different lactation stages, as only 1314 circRNAs were detected in both libraries. Majority of the candidate circRNAs maps to intronic and intergenic regions, namely noncoding regions. There existed the circular preference or specificity of some genes. Interestingly, 4 protein coding genes (Rev3l, IGSF11, MAML2, and LPP) that also tanscripted high level circRNAs have been reported to be involved in cancer. The distribution of specific miRNA binding sites and RNA binding proteins binding sites also implied the role of circRNAs in mammary gland development and tumorigenesis. Conclusions:The results provide the basis for comparisons with breast cancer profiles and for selection of representative circRNA candidates for future functional characterization in breast development and breast cancer.
2017-08-20 | GSE60539 | GEO
Project description:To identify genes specifically expressed in lactating mammary glands, the gene expression profiles of luminal and basal cells from different developmental stages were compared. Comparison of gene expression in luminal and basal cells harvested from the mammary glands of virgin, 18.5 day pregnant and 2 day lactating mice (2 mice per stage).
2015-01-19 | E-GEOD-60450 | biostudies-arrayexpress
Project description:To identify genes specifically expressed in lactating mammary glands, the gene expression profiles of luminal and basal cells from different developmental stages were compared.
2015-01-19 | GSE60450 | GEO
Project description:This is the Unlabelled
model as described in:
Simulation of the Pentose Cycle in Lactating Rat Mammary Gland
Haut MJ , London JW , Garfinkel D Biochem J.
1974,138(3), 511-524. PMID: 4154746
;PMCID: PMC1166237
Abstract:
A computer model representing the pentose cycle, the tricarboxylic acid cycle and glycolysis in slices of lactating rat mammary glands has been constructed. This model is based primarily on the studies, with radioactive chemicals, of Abraham and Chaikoff (1959) [although some of the discrepant data of Katz and Wals (1972) could be accommodated by changing one enzyme activity]. Data obtained by using [1-(14)C]-, [6-(14)C]- and [3,4-(14)C]-glucose were simulated, as well as data obtained by using unlabelled glucose (for which some new experimental data are presented). Much past work on the pentose cycle has been mainly concerned with the division of glucose flow between the pentose cycle and glycolysis, and has relied on the assumption that the system is in steady state (both labelled and unlabelled). This assumption may not apply to lactating rat mammary glands, since the model shows that the percentage flow through the shunt progressively decreased for the first 2h of a 3h experiment, and we were unable to construct a completely steady-state model. The model allows examination of many quantitative features of the system, especially the amount of material passing through key enzymes, some of which appear to be regulated by NADP(+) concentrations as proposed by McLean (1960). Supplementary information for this paper has been deposited as Supplementary Publication SUP 50023 at the British Museum (Lending Division) (formerly the National Lending Library for Science and Technology), Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1973) 131, 5.
All reactions are modelled as mass action, reactions labelled 1-30 in the order they appear in Scheme 1. Note that the unit of substance is micromole per 0.5g wet weight of tissue. Simulation reproduces results in tables 5 and 6.
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.
.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
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Project description:Cross-species hybridization analysis of mammary glands during pregnancy and lactation. Results provide insight into putative conserved molecular mechanisms regulating mammary gland development. This study was performed to identify orthologous transcripts that are differentially co-expressed in the mammary gland at 2 stages of development (pregnancy and lactation) in wild type Sprague-Dawley rats. Key points are examined in a time series of Sprague Dawley rat mammary gland development, secretory activation and lactation. Triplicate rat (three biological replicates) at each time point were used for statistical power totalling 12 individual arrays in this study. Rats were as staged pregnant day 1 the day that post coital plug was observed, and similarly, lactation day 1 was the first day after birth. Whole mammary glands No. 4 (inguinal) were obtained from female rats at stages of development: virgin (adulthood, 14 wks of age), Pregnant (5 and 14 days of pregnancy) and Lactating (day 1 and 12 postpartum). The two-color (Cy5/Cy3) microarray experiment was designed to hybridize samples from each group against a common reference, a pool of RNA from mammary gland of three parous or virgin female rats.
2013-10-30 | E-GEOD-22545 | biostudies-arrayexpress
Project description:This study was performed to identify transcripts that are differentially expressed in the mammary gland at 4 stages of developmental (virgin, pregnant, lactating and involution) in wild type C57BL/6J mice. Experiment Overall Design: Whole mammary glands No4 (inguinal) were obtained from female mice at 4 stages of development: Virgin (puberty, 6 wks of age), Pregnant (14 days of pregnancy), Lactating (day 10 postpartum) and Involution (4 days post weaning of pups). Three biological replicates were obtained from Virgin females and two biological replicates for the three other stages. mice
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Project description:Nutrition affects milk composition influencing its nutritional properties. Nutrition also modifies the expression of mammary genes, whose regulation is not completely known. MicroRNAs (miRNA) are small non-coding RNA that work as important post-transcriptional gene expression regulators by targeting messenger RNAs. Our goal was to characterize miRNA whose expression is regulated by nutrition in the lactating goat mammary gland, and which may give clues to decipher the regulations of milk components biosynthesis and secretion. Using high-throughput sequencing technology, miRNomes of the lactating mammary gland have been established from 4 goats fed ad libitum and 6 goats food deprived during 48h. Food deprivation affected the expression of 30 miRNA (padj<0.1), 16 were downregulated and 14 were upregulated. Prediction tools Diana-microT suggests a potential role of several nutriregulated miRNA in the lipid metabolism. Among putative targets 19 differently expressed genes (DEG) previously identified in the same sample, were found. Functions of these 19 DEG revealed their involvement in tissue remodeling. This study constitutes the first evidence of nutriregulated miRNA in the ruminant mammary gland. The characterization of these 30 miRNA could contribute to a better understanding of genes regulations in the mammary gland in response to nutrition. MicroRNA profiles of mammary glands from 10 Alpine goats at the peak of lactation (48 ± 2 days post-partum) generated by a HiSeq 2500 using Illumina Solexa technic.
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Project description:The goal of this study is to improve the quality, efficiency, and sustainability of milk production by improving the understanding of the function of cis-regulatory elements in regulating the bovine mammary gland. To this end, we have characterized the non-lactating and lactating mammary gland transcriptomes by whole transcriptome shotgun sequencing (RNA-seq). We will identify cis-regulatory elements in the non-lactating and lactating bovine mammary gland genome-wide. Finally, we will annotate and characterize mammary gland cis-regulatory elements by computational analysis and identify high-resolution genome-wide in vivo footprints of diverse trans-acting-factors (TF), over-represented TF bindings sites and overlapping SNPs.
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Project description:Identify and characterize the circular RNAs expressed in in the half-smooth tongue sole (Cynoglossus semilaevis)
| PRJNA407884 | ENA