Project description:To identify substrates of the ubiquitinating E3 enzyme Rsp5 we applied purified Rsp5 to duplicate protein arrays. The Rsp proteins were expressed as fusion proteins to GST. We used as a control Ubr1, a RING domain containing E3 ligase We analyzed Rsp5 from S.cerevisiae on duplicate arrays, with four control chips, two without Rsp5 and two with Ubr1.
Project description:Peripheral blood monocytes were differentiated into macrophages, starved for 24h hours, and treated for 3h with LPA 18:0, 20:4 or a mix of LPAs similar to the composition in ascites (1 µM 16:0 + 0.25 µm 18:0 + 0.5 µM 18:1 + 1.625 µM 18:2 + 1.625 µM 20:4). RNA expression was measured via QuantSeq.
Project description:This SuperSeries is composed of the following subset Series: GSE24037: Salivary cytokine alterations in HIV infection part 1 GSE24064: Salivary cytokine alterations in HIV infection part 2 Refer to individual Series
Project description:Runt domain (Runx) transcription factors constitute a metazoan family of sequence specific DNA binding proteins that are essential for animal development. The sea urchin Runx gene SpRunt-1, which is expressed globally during early embryogenesis, is required for blastula stage cell proliferation and subsequently for cell survival. To obtain a comprehensive list of SpRunt-1 regulatory targets we screened a custom microarray representing the blastula stage transcriptome of Strongylocentrotus purpuratus, comparing relative hybridization signals generated by labeled RNA from 18 hr control versus SpRunt-1 morphant embryos. For an 8x15k chip the 8 arrays were 4 biological replicates and a dye swap of the same 4. Biological Replicates - Four separate embryo cultures, each from a different mating pair were initiated and divided into a control group and a treatment group. All of the embryos in the treatment group were micoinjected with a splice-blocking morpholino antisense oligonucleotide (MASO) targeted to SpRunt-1. All control and sample embryos were developed to hatched blastula stage (18 hours post-fertilization) in filtered seawater at 15°C. Total RNA was extracted from each of the four separate samples (3,600 embryos in each sample) with an RNA yield near 5 micro grams per sample. Total RNA was also extracted from the untreated embryos of each separate culture pooled together (about 14,400) with an RNA yield near 20 micro grams. Technical (dye swap) Replicates - Control derived Cy3 (green) labeled aRNA was mixed with sample derived Cy5 (red) labeled aRNA in one biological replicate set of 4 samples and using half of the extracted RNA amount. The other half of the RNA was reciprocally labeled with control derived aRNA Cy5 labeled and sample derived aRNA Cy3 labeled.
Project description:Screening of 22 novel proteins derived from Campylobacter jejuni NCTC 11168 identified prior via screening of cDNA libraries. The full-length proteins were attached using a specific HaloTag to their corresponding ligand surface, HaloLink. Screening was performed using three different polyclonal antibodies to Campylobacter jejuni and detection was achieved by goat polyclonal antibody to rabbit IgG conjugated with Chromeo-546. In order to assess their potential immungenic nature and rank the proteins investigated, comparative analysis using already described antigens from C. jejuni were used in the assay. Each microarray was separated into different incubation chambers using the ProPlate (Grace Biolabs) multi-well gaskets. While for two slides (2009 and 2447), three chambers were used, the remaining slides were designed to use 16 different compartments. Each compartment could be incubated with different antibodies and represent individual replicates of the slides. As positive references, hisJ and cjaA were used. For negative controls, argC and gapA were used, and the crude lysates of the expression host (Acella E. coli) and buffer were spotted as well. For slides 2009 and 2447, three-well gaskets were used allowing for seven replicates per sample, while only incubation with one antibody. Slides 416033 and 416826 used 16-well gaskets and only hisJ and argC as protein references. Samples and controls were spotted in quadruplicate. Finally, for 1000 and 1001, samples were spotted in triplicate, whereas controls were spotted in quadruplicate using hisJ, cjaA, argC and gapA as protein references.
Project description:Fetal lung development is a complex biological process, which involves temporal and spatial regulations of many genes. To understand molecular mechanisms of this process, we investigated gene expression profiling of lungs at gestational day 18, 19, 20, 21, new born, and adult rats using in-house rat DNA microarray containing 6,000 known genes and 4,000 ESTs. 1,512 genes passed SAM test and 583 genes (402 known genes and 181 ESTs) had a 2-fold change at least at one time point. K-means cluster analysis revealed 7 major expression patterns. Furthermore, using GeneMapp, we identified 3 regulatory pathways: TGF beta signaling pathway, cell cycle, and G-protein signaling; and 2 metabolism pathways: proteasome degradation and glycolysis. Our results suggest a complex regulatory pathway for fetal lung development. Loop Design as following: D18-D19-D20-D21-NB-AD-D18