6af85ae1-8aa4-4482-9ca0-882a0c53c70e - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001006368 | EGA |
REPOSITORIES: EGA
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Project description:Assessment of sources of non-biological (technical) variability in the processing of RNA samples and gene chips during microarray analysis. The purpose of this experiment was to measure technical variability in microarray data introduced by various steps in preparation of the RNA, amplification/labeling of the RNA and hybridization of the sample to the arrays on separate days. The experimental design utilized a single tissue source - homogenized brain tissue pooled from 3 eight week old male C57/Bl mice. Variables examined include: I) Technician extracting RNA (technician #1 prepared Pools 1 and 2; technician #2 prepared pools 3 and 4). II) RNA extraction (Pools 1-4 represent four independent RNA extractions from 3 homogenized pooled whole mouse brains from 8 week old male C57/B6 mice) III) Independent RNA labeling/amplification reactions - three performed from each RNA pool labeled A, B and C) and IV) Day of hybridization to GLYCOv1 arrays (labeled samples were hybridized to arrays over 3 days - 11/14/02, 11/15/02 and 11/18/02). 32 samples made it through to completion generating a high quality .CEL file for analysis. Four samples failed at various steps in the preparation/hybridiztion. All samples were male 8 week old C57/Bl mouse brain total RNA.
2010-12-11 | E-GEOD-26008 | biostudies-arrayexpress
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Project description:A library of transposon mutants was generated in Salmonella enterica serovar Typhimurium strain SL1344 using custom Tn5 and Mu transposons with outward-facing T7 and SP6 promoters. The library was grown up in vitro, and used as the input pool for mouse infection experiments. An in vivo output pool was obtained from the mouse livers 2 days post-infection.<br><br>Genomic DNA was extracted from the input and output pools and digested with the restriction enzyme RsaI. Cy5-labelled RNA run-offs were produced seperately from the T7 and SP6 promoters and hybridised to a tiling microarray along with the Cy3-labelled in vitro transcription products from an untransposed SL1344 wild type control. Analysis of the microarray data allows the location of the transposon inserts to be determined. Mutants that are present in the input pool but that are absent or less prevalent in the output pools are inferred to be attenuated in vivo.
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Project description:In mammalian cells, the catabolic activity of the dNTP triphosphohydrolase SAMHD1 sets the balance and the concentrations of the four dNTPs. Deficiency of SAMHD1 leads to unequally increased pools and marked dNTP imbalance. Although it is documented that imbalanced dNTP pool expansion increases mutation frequency in cancer cells, it is not known if the SAMHD1-induced dNTP imbalance favors accumulation of somatic mutations in non-transformed cells. Here we have investigated how fibroblasts isolated from Aicardi Goutières Syndrome (AGS) patients with mutated SAMHD1 react to the constitutive pool imbalance characterized by a huge dGTP pool. We focused on the effects on dNTP pools, cell-cycle progression, dynamics and fidelity of DNA replication, efficiency of UV-induced DNA repair. AGS fibroblasts entered senescence prematurely or upregulated genes involved in G1/S transition and DNA replication. The normally growing AGS cells exhibited unchanged DNA replication dynamics and, when quiescent, faster rate of excision repair of UV-induced DNA damages than wildtype fibroblasts. To investigate if the lack of SAMHD1 affects DNA replication fidelity we compared de novo mutations in AGS and WT cells by exome next generation sequencing. Somatic variant analysis indicated a mutator phenotype suggesting that SAMHD1 is a caretaker gene whose deficiency is per se mutagenic promoting genome instability in non-transformed cells.
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Project description:ChIP-on-Chip experiment using chromatin from wild-type 5 weeks old swiss mice ovaries (Nishi et al, 2001) and an isovolumic blend of our custom anti-Foxl2 polyclonal antibodies (Cocquet J et al, 2002). Non precipitated sheared matched deproteinized chromatin (Input) was used a control to estimate genomic enrichment peaks (and thus Foxl2 binding sites) from IPed DNA. DNA from three independent ChIP assays (Input extractions) was pooled, and 100ng of DNA was linearly amplified using the Whole Genome Amplification kit (Sigma).
2011-02-22 | E-MTAB-400 | biostudies-arrayexpress
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Project description:The potential for xenoestrogens and other environmental chemicals to alter female reproductive function calls for the study of their affects on endogenous hormone-regulated gene expression pathways during uterine tissue remodeling which occurs as part of the menstrual/estrus cycle. However, our knowledge of these pathways is limited. Here, we characterize changes in the CD-1 mouse uterine transcriptome during proestrus and estrus, which are regulated by estrogen and progesterone in preparation of the uterus for pregnancy. Mice were staged beginning at 6 wk of age and uterine horns were harvested after monitoring two estrus cycles. Microarray analysis identified 2,429 genes differentially expressed in estrus compared to proestrus, indicating that the mouse uterus undergoes remarkable remodeling during the estrus cycle, affecting ~10% of all protein-coding genes. Changes in gene expression associated with structural alteration of the uterus include remodeling of the extracellular matrix, changes in cell keratins and adhesion molecules, activation of mitosis, MHC class II presentation, complement and coagulation cascades, and cytochrome P450 expression. Signaling pathways regulated during the estrus cycle, involving ligand-gated channels, Wnt and hedgehog signaling, and several transcription factors with poorly understood roles in reproductive tissues, include several genes and gene networks that have been implicated in pathological states. The information presented here builds a background for understanding of mechanisms involved in uterine tissue response to endocrine disruptors and the development of reproductive tract diseases. Beginning on postnatal day 42, female CD-1 mice were monitored for reproductive stage cycle for 2 consecutive cycles and then total RNA was isolated from uterine horns at estrus or proestrus. Samples were pooled for microarray as follows. Six litters were used to generate 2 tissue pools for estrus and 2 tissue pools for proestrus, with estrus pool 1 and proestrus pool 1 comprised of mice from the same 3 litters, and estrus pool 2 and proestrus pool 2 comprised of mice from the other 3 litters. Each pool was comprised of uterine tissue RNA from n= 4-6 individual mice. Fluorescent labeling of RNA and hybridization of the Alexa 555-labeled (green) and Alexa 647-labeled (red) RNA samples to Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 (Agilent Technology, Palo Alto, CA; catalog # G4846A) were carried out, with dye swapping for each estrus cycle stage comparison.
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