Journal: PLoS ONE

Article Title: Somatic Donor Cell Type Correlates with Embryonic, but Not Extra-Embryonic, Gene Expression in Postimplantation Cloned Embryos

doi: 10.1371/journal.pone.0076422

Figure Lengend Snippet: List of samples from E6.5 cloned embryos analyzed by microarray.

Article Snippet: Amplified RNA was labeled with Cy3 dye (GE Healthcare UK Limited, Buckinghamshire, England) and hybridized to a whole mouse genome oligo DNA microarray (4×44 K, Agilent Technologies, Palo Alto, CA, USA) for 17–18 h at 65°C.

Techniques: Clone Assay, Microarray

Journal: PLoS ONE

Article Title: Somatic Donor Cell Type Correlates with Embryonic, but Not Extra-Embryonic, Gene Expression in Postimplantation Cloned Embryos

doi: 10.1371/journal.pone.0076422

Figure Lengend Snippet: ( A ) Embryos were retrieved at E6.5 (left) and dissected into four parts (right). EPC, ectoplacental cone; VE, visceral endoderm; EXE, extraembryonic ectoderm; EPI, epiblast. Scale bar = 100 µm. B) Raw signal values of Pou5f1 (left), Cdx2 (center) and Pgk1 (right) genes extracted from microarray data. Pou5f1 and Cdx2 were detected exclusively in the embryonic and extraembryonic samples, respectively, while Pgk1 was detected in both samples. These results confirmed the accuracy of sample preparation from the embryonic and extraembryonic tissues. Em, embryonic samples; Ex, extraembryonic samples; IVF, samples from in vitro fertilized control embryos; CC, cumulus cell-derived clone; FC, fibroblast-derived clone; SC, Sertoli cell-derived clone. See Figure S2 for further validation by several other marker genes.

Article Snippet: Amplified RNA was labeled with Cy3 dye (GE Healthcare UK Limited, Buckinghamshire, England) and hybridized to a whole mouse genome oligo DNA microarray (4×44 K, Agilent Technologies, Palo Alto, CA, USA) for 17–18 h at 65°C.

Techniques: Microarray, Sample Prep, In Vitro, Derivative Assay, Marker

Journal: PLoS ONE

Article Title: SIRT6 Is Required for Normal Retinal Function

doi: 10.1371/journal.pone.0098831

Figure Lengend Snippet: Whole retina mRNA from WT and KO mice was used to profile the expression of several key genes of glutamate receptors involved in the synaptic transmission in an Affymetrix Mouse Gene 2.1 ST DNA microarray. a) Heatmap representing the hierarchical cluster analysis shows the differential expressed mRNAs between WT and SIRT6 KO retinas. The graphic depicts the expression levels of ionotropic AMPA glutamate receptors (Gria1–4), Glutamate receptor, ionotropic kainate (Grik1-2-4-5), Glutamate [NMDA] receptors (Grin1-2a-c) and metabotropic glutamate receptors (Grm1–8). The expression data for the hierarchical clustering image has been row normalized to a range of zero to one with blue representing the row minimum and red representing the row maximum. b) RNA was purified from SIRT6 WT and KO retinas, and Grm6 levels analyzed by RT-PCR. c) immunofluorescence was performed in SIRT6 WT and KO retinas with the indicated antibodies. PKC-alpha was used as a marker for ON bipolar cells. Ganglion Cell Layer (GCL), Inner Plexiform Layer (IPL), Inner nuclear Layer (INL), Outer Plexiform Layer (OPL), Outer Nuclear Layer (ONL), Retinal Pigment Epithelium (RPE). Data are mean ± SE (n = 4) **p<0.01 d) Representative fluorescent images of TUNEL analysis performed in WT and SIRT6 KO retinal sections. Apoptotic nuclei (bright green dots) labeled with fluorescein-dUTP were visualized by fluorescence microscopy. Data are mean ± SE (n  = 3) **p<0.01

Article Snippet: Whole retina mRNA from SIRT6 WT and KO mice (n = 3 from each condition) was hybridized onto an Affymetrix Mouse Gene 2.1 ST DNA microarrays.

Techniques: Expressing, Transmission Assay, Microarray, Purification, Reverse Transcription Polymerase Chain Reaction, Immunofluorescence, Marker, TUNEL Assay, Labeling, Fluorescence, Microscopy