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Displaying 20 of 130 results for "TSC22D3"
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  1. Genome-wide analysis reveals TET- and TDG-mediated 5-methylcytosine oxidation dynamics [MeDIP-Seq] ArrayExpress

    ID: E-GEOD-46111

    Description: Ten-eleven translocation (Tet) family of DNA dioxygenases converts 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5- carb...

  2. Reconstruction of the dynamic regulatory network that controls Th17 cell differentiation by systematic perturbation in primary cells (ChIP-Seq) OmicsDI

    ID: E-GEOD-43949

    Date Released: 05-04-2014

    Description: the differentiation of Th17 cells. DNA binding of TSC22D3 in Th17 cells compared to WCE...

  3. Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics BioProject

    ID: PRJNA243290

    Keywords: Epigenomics

    Access Type: download

    dataset.description: in various human pathologies. In mammals, the TET family of dioxygenases can oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) in a stepwise manner. 5fC and 5caC are selectively recognized and excised by mammalian thymine DNA glycosylase (TDG), and ...
  4. A library of yeast transcription factor motifs ArrayExpress

    ID: E-GEOD-12349

    Description: s Protein binding microarray (PBM), ChIP-chip and DIP-chip experiments of yeast transcription factor DNA-binding domains were performed. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to custom-designed, double-stranded 44K Agilent microarrays in order to determine their sequence preferences. The method is described in Berger et al., Nature Biotechnology 2006. A key feature is that the microarrays are composed of de Bruijn sequences that contain each 10-base sequence once and only once, providing an evenly balanced sequence distribution. Individual de Bruijn sequences have different properties, including representation of gapped patterns. Here we provide the data transformed into median intensities for all 32,896 8-base sequences, Z-scores for these intensities, and E-scores. E-scores are a modified version of AUC, and describe how well each 8-mer ranks the intensities of the spots. In general the E-scores are slightly more reproducible than Z-scores, but contain less information about relative binding affinity. Additional experimental details are found in Berger et al., Nature Biotechnology 2006, Berger et al., Cell 2008, and the accompanying Supplementary information. Raw 35-mer array data is available on the web link provided...

  5. interphalangeal (PIP) and distal interphalangeal (DIP) joints for the shod (n=4) and unshod (n=4) conditions about the flexion-extension axis... PeerJ

    ID: doi:10.7287/PEERJ.PREPRINTS.1779/SUPP-4

    Release Date: 02-23-2016

    Creators: Panagiotopoulou, Olga

  6. Epigenetic and transcriptional landscapes of Dnmt3a-deficient olfactory sensory neurons ArrayExpress

    ID: E-GEOD-52464

    Description: SN-expressed genes, and the alteration of odorant-induced transcriptional responses of immediate early genes. Together, these results demonstrate that Dnmt3a is necessary to define the neuronal transcriptional state and may be broadly involved in refining expression profiles within differentiated cells. To determine the contributions of Dnmt3a to the DNA modification and transcriptional landscapes of a post-mitotic neuronal population, we performed DNA immunoprecipitation (DIP-seq) using antibodies specific for 5mC and 5hmC and rRNA-depleted transcriptional profiling (RNA-seq) coupled to high-throughput sequencing using genomic DNA or RNA from FACS-isolated mature olfactory sensory neurons (mOSNs) from main olfactory epithelium (MOE) of Dnmt3a wildtype (WT), heterozygous-null (Het), or homozygous-null (KO) 3-week old mice. Similarly, to compare this information with other epigenetic features of the MOE, we performed H3K4me1 (WT), H3K27ac (WT), and H3K27me3 (WT and K...

  7. Complementary Expression of Immunoglobulin Superfamily Ligands and Receptors in Synaptic Pairs in the Drosophila Visual System ArrayExpress

    ID: E-GEOD-68235

    Description: gging, we demonstrate that 21 paralogs of the Dpr family, a subclass of Immunoglobulin (Ig)-domain containing proteins, are expressed in unique combinations in homologous neurons with different layer-specific synaptic connections. Dpr interacting proteins (DIPs), comprising nine paralogs of another subclass of Ig superfamily proteins, are expressed in a complementary layer-specific fashion in a subset of synaptic partners. We propose that pairs of Dpr/DIP paralogs contribute to layer-specific patterns of synaptic connectivity. Conclusions: This complexity is mirrored by the complexity of the cell surface and secreted molecules expressed by each of the R cell and lamina neurons profiled in this study. How this complexity contributes to specificity remains elusive, but the ...

  8. interphalangeal (PIP) and distal interphalangeal (DIP) joints for the shod (n=4) and unshod (n=4) conditions about the flexion-extension axis... PeerJ

    ID: doi:10.7287/PEERJ.PREPRINTS.1779V1/SUPP-4

    Release Date: 02-23-2016

    Creators: Panagiotopoulou, Olga

  9. Transcriptome response to change in ploidy level in Arabidopsis BioProject

    ID: PRJNA99151

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: developmental stage1.02, 2 leaves). Sample names: DIP diploid TET tetraploid TFE triploid female excess TME triplod male excess Experimenter name: Olivier Garnier Experimenter phone: 00-353-21-490-4028 Experimenter address: Plant molecular genetics lab, Dpt of Biochemistry, UCC Experimenter address: Lee Maltings Prospect row Experimenter zip/postal_code: Cork Experimenter country: Ireland Keywords: strain_or_line_design Overall design: 11 samples were used in this experiment...
  10. Structural elucidation of a novel mechanism for bacteriophage-based inhibition of the RNA degradosome OmicsDI

    ID: PXD003285

    Date Released: 01-01-1000

    Description: ected cell. Encoded by the giant phage фKZ, KZ37/Dip associates with two RNA binding sites of the RNase E component of the Pseudomonas aeruginosa RNA degradosome. Thereby, KZ37/Dip competes with the binding of RNA substrates, resulting in effective inhibition of RNA degradation. The crystal structure of KZ37/Dip (2.2 Å) reveals an unprecedented fold for which there are no identified structural homologues. The protein forms a homo-dimer th...

  11. Crystal structure of gp37(Dip) from bacteriophage phiKZ PDB

    ID: PDB:5FT0

    Description: GP37

  12. Genome-wide analysis of expression and DNA methylation at CpG-island-associated sense-antisense transcript loci in mouse BioProject

    ID: PRJNA111365

    Keywords: Other

    Access Type: download

    dataset.description: .5 and 13.5 days postcoitum (dpc)]) were used for DIP chip experiments. Nine of twelve tissues were separately analyzed classified on the basis of sex. A technical duplication of DIP chip analysis was performed by using the same genomic DNA of male kidney....
  13. Crystal structure of gp37(Dip) from bacteriophage phiKZ bound to RNase E of Pseudomonas aeruginosa PDB

    ID: PDB:5FT1

    Description: GP37, RIBONUCLEASE E (E.C.3.1.26.12)

  14. Novel targets for the transcription factors MEF2 in MA-10 Leydig cells OmicsDI

    ID: E-GEOD-64128

    Date Released: 04-18-2015

    Description: e Pde8a, Por, Ahr, Bmal1, Cyp1a1, Cyp1b1, Map2k1, Tsc22d3, Nr0b2, Smad4, and Star, which were all downregulated in the absence of MEF2. In silico analyses revealed the presence of MEF2 binding sites within the first 2 kb upstream the transcription start site of the Por, Bmal1, and Nr0b2 promoters, which suggests a direct regulation by MEF2. Using transient transfections in MA-10 Leydig cells, siRNA knockdown, and a MEF2-Engrailed dominant negative, we found that MEF2 activates the Por, Bmal1 and Nr0b2 promoters and that this requires an intact MEF2 element. Our results identify novel target genes for MEF2 and define MEF2 as an important regulator of Leydig cell function and male reproduction. MA-10 Leydig cells were treated with siRNA MEF2A/2D (siRNA MEF2) or scrambled siRNA as control (siRNA Ctrl) 48h before total RNA extraction....

  15. Novel targets for the transcription factors MEF2 in MA-10 Leydig cells BioProject

    ID: PRJNA270224

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: e Pde8a, Por, Ahr, Bmal1, Cyp1a1, Cyp1b1, Map2k1, Tsc22d3, Nr0b2, Smad4, and Star, which were all downregulated in the absence of MEF2. In silico analyses revealed the presence of MEF2 binding sites within the first 2 kb upstream the transcription start site of the Por, Bmal1, and Nr0b2 promoters, which suggests a direct regulation by MEF2. Using transient transfections in MA-10 Leydig cells, siRNA knockdown, and a MEF2-Engrailed dominant negative, we found that MEF2 activates the Por, Bmal1 and Nr0b2 promoters and that this requires an intact MEF2 element. Our results identify novel target genes for MEF2 and define MEF2 as an important regulator of Leydig cell function and male reproduction. Overall design: MA-10 Leydig cells were treated with siRNA MEF2A/2D (siRNA MEF2) or scrambled siRNA as control (siRNA Ctrl) 48h before total RNA extraction....
  16. Crystal structure of Alkylhydroperoxide Reductase subunit F from E. coli at 2.65 Ang resolution PDB

    ID: PDB:4O5U

    Description: Alkyl hydroperoxide reductase subunit F (E.C.1.8.1.-)

    dataset.creators: Dip, P.V.
  17. Crystal structure of Alkylhydroperoxide Reductase subunit C from E. coli PDB

    ID: PDB:4O5R

    Description: AhpC component, subunit of alkylhydroperoxide reductase (E.C.1.8.1.-, 1.11.1.15)

    dataset.creators: Dip, P.V.
  18. An Insight Into Simulated Product Development: Lotus Stem Dip Figshare

    ID: doi:10.6084/M9.FIGSHARE.1520396

    Release Date: 08-26-2015

    Description:

  19. TIP_ANTMA UniProt:Swiss-Prot

    ID: P33560

    Description: ype Helical; Name=1 Helical; Name=2 Helical; Name=3 Helical; Name=4 Helical; Name=5 Helical; Name=6 NPA 1 NPA 2...

  20. Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis (MeDIP-seq) BioProject

    ID: PRJNA255657

    Keywords: Epigenomics

    Access Type: download

    dataset.description: pression profiles and hallmarks of human AML1-ETO induced AML. Using this model, we show that the primary effect of Tet2 loss in pre-leukemic hematopoietic cells is progressive and widespread DNA hypermethylation affecting up to 25% of active enhancer elements. In contrast, CpG island and promoter methylation does not change in a Tet2-dependent manner, but increase relative to population doublings. We confirm this specific enhancer hypermethylation phenotype in human AML patients with TET2 mutations. Analysis of immediate gene expression changes reveals rapid deregulation of a large number of genes implicated in tumorigenesis, includin...

Displaying 20 of 130 results for "TSC22D3"