Benzo-a-pyrene induced miRNA changes in mouse
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: jie zuo
PROVIDER: E-MTAB-2407 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description: Not available
2012-06-01 | E-MTAB-80 | biostudies-arrayexpress
Project description:modENCODE_submission_2971 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: RNA-seq EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: w1118; Developmental Stage: 2-18hr embryo; Genotype: w[1118]; EXPERIMENTAL FACTORS: Developmental Stage 2-18hr embryo; Strain w1118
2010-10-18 | E-GEOD-24540 | biostudies-arrayexpress
Project description:modENCODE_submission_2973 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: RNA-seq EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: S2-Rubin; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male; EXPERIMENTAL FACTORS: Cell Line S2-Rubin
2010-10-18 | E-GEOD-24542 | biostudies-arrayexpress
Project description:modENCODE_submission_2974 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: RNA-seq EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: Kc-Rubin; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female; EXPERIMENTAL FACTORS: Cell Line Kc-Rubin
2010-10-18 | E-GEOD-24543 | biostudies-arrayexpress
Project description:Protein-protein proximity of core pluripotency transcription factors plays an important role during cell reprogramming. Pluripotent embryonic stem (ES) cell identity is controlled by a trio of transcription factors: Sox2, Oct4, and Nanog. These proteins often bind to closely localized genomic sites. The precise mode by which Sox2, Oct4, and Nanog interact with DNA is likely to make a crucial contribution to their function. Here, a detailed protocol for in vivo detection and quantitative analysis of protein-protein proximity of Sox2 and Oct4 using Proximity Utilizing Biotinylation (PUB) method based on the use of the BAP/BirA (target/enzyme) system is described. The method includes design and cloning of DNA plasmid construct, transient transfection of HEK293T cells, Western blot analysis of nuclei fraction and LC-MS/MS analysis. Experiments with coexpression of BAP-X+BirA-Y (X, Y=Sox2, Oct4 and GFP as control) revealed strong biotinylation level of target proteins when X and Y were pluripotency transcription factors compared with control when X=GFP. Since mass spectrometry provides both high sensitivity and more accurate quantification of data a modified workflow was used, in which SDS-PAGE step was eliminated and His-tagged BAP-fused proteins from cell lysate were purified in 6M guanidine HCl buffer, washed, propionylated, digested directly on the Ni sepharose beads using trypsin and analysed on Q-TOF Impact II instrument. Using mass spectrometry allows making quantitative estimation of in vivo interaction of BAP-Sox2 and BirA-Oct4 which was demonstrated by measuring ratios of biotinylation levels of BAP fused either with Sox2 or GFP at different biotin pulse times. After vector preparation this protocol can be completed in seven working days.
2020-01-21 | PXD015756 | Pride
Project description:modENCODE_submission_2972 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: RNA-seq EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: w1118; Developmental Stage: 2-18hr embryo; Genotype: w[1118]; EXPERIMENTAL FACTORS: Developmental Stage 2-18hr embryo; Strain w1118
2010-10-18 | E-GEOD-24541 | biostudies-arrayexpress
Project description:Bees from 3 unrelated colonies were injected with 1ul PBS extract containing 10^9 genome equivalent of Deformed wIng virus (DWV) and/or fed 10µl sucrose solution containing 10^5 fresh Nosema ceranae spores. Control bees were injected and fed with an equivalent DWV- and Nosema-free extract respectively). Bees were kept in cages of 21 bees (7 from each colony), and each cage was replicated 5 times per each of the 4 treatments). Bess were kept in an incubator at 30°C/50%RH. At day 12 p.i., bees were flash frozen in liquid nitrogen, and stored at -80°C. Bee abdomen RNA was sent to Christina Grozinger lab (Penn State, USA). RNA was pooled for 3 abdomens per replicate for 5 replicates per treatment. Arrays were hybridized in a dye-swap loop design.
2017-03-08 | E-MTAB-5508 | biostudies-arrayexpress
Project description:High-throughput gene expression profiling has become an important tool for investigating transcriptional activity in a variety of biological samples. To date, the vast majority of these experiments have focused on specific biological processes and perturbations. Here, we have generated and analyzed gene expression from a set of samples spanning a broad range of biological conditions. Specifically, we profiled gene expression from 91 human and mouse samples across a diverse array of tissues, organs, and cell lines. Because these samples predominantly come from the normal physiological state in the human and mouse, this dataset represents a preliminary, but substantial, description of the normal mammalian transcriptome. We have used this dataset to illustrate methods of mining these data, and to reveal insights into molecular and physiological gene function, mechanisms of transcriptional regulation, disease etiology, and comparative genomics. Finally, to allow the scientific community to use this resource, we have built a free and publicly accessible website (http://expression.gnf.org) that integrates data visualization and curation of current gene annotations. The terms of the Novartis data release policy prevent us from redistributing .cel files for this experiment, therefore there is no raw data, we hope to be able to release this in future.
2002-03-19 | E-MEXP-18 | biostudies-arrayexpress
Project description:Wild type or Cd27-/- mice of 8-12 weeks old were immunized intranasally with 500 ug ovalbumin (OVA) protein and 1 ug cholera toxin in 50 ul HBSS. Spleen, draining lymph node (DLN) or lung were isolated at day 3, day 4 or day 8 after immunization. Single cell suspensions of indicated organs were prepared and OT-I T cells were isolated from this using flow cytometric cell sorting.
2013-08-18 | E-MTAB-1772 | biostudies-arrayexpress
Project description:modENCODE_submission_2834 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: RNA-seq EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Ago2 414; Tissue: Adult ovaries; Developmental Stage: Adult Female; Genotype: w;;ago2[414]; Sex: Female; EXPERIMENTAL FACTORS: Tissue Adult ovaries
2010-10-17 | E-GEOD-24317 | biostudies-arrayexpress