Project Achilles Copy Number Paper by Robin Meyers (2819002)

“…</div><div><br></div><div><br></div><div><br></div><div>Analysis steps v3.3.8a:</div><div><br></div><div>1. QC and identify reps with reproducibility <0.8 or are outliers on PCA or fail FP</div><div>2. remove sgRNAs(guides) with low counts in DNA samples:</div><div>completely remove shRNAs with median <=1 </div><div>3. remove replicates that fail QC measures </div><div>4. fold change(FC) with DNA pool samples </div><div>5. zero-center median of negative controls</div><div>6. collapse replicates per line </div><div>7. sgRNAs are mapped to genes using(Achilles_v3.3.8a.gct)</div><div><br></div><div>Analysis steps v3.3.8:</div><div><br></div><div>1. …”

Effect of Mediator disruption on euchromatic genes. by Eriko Oya (446107)

“…<p>Venn diagram showing the number of transcripts whose expression levels are increased (up) or decreased (down) >1.5-fold in mutants compared to the wild-type. …”

Performance of RFECS for enhancer predictions in H1 and IMR90 cells. by Nisha Rajagopal (389555)

“…<p>Area under the 5-fold cross-validated ROC curve decreases with increase in number of trees stabilizing gradually in A.)H1 and B.)IMR90 cells. …”

Spf1 affects the cellular distribution of Mn²⁺. by Yifat Cohen (504564)

“…By looking at the fold change of ion concentration of Δ<i>spf1</i> or OE-Spf1 microsomes relative to WT it can be seen that Mn²⁺ is the only ion that decreases in Δ<i>spf1</i> and increases in microsomes of OE-Spf1. …”

Differential Regulation of Extracellular Matrix and Soluble Fibulin-1 Levels by TGF-β₁ in Airway Smooth Muscle Cells by Ling Chen (25698)

“…<div><p>Fibulin-1 (FBLN-1) is a secreted glycoprotein that is associated with extracellular matrix (ECM) formation and rebuilding. …”

Contrasting transcriptomes of somatic, OSKM transduced HFF1 and pluripotent cell types. by Nancy Mah (105583)

“…The normalized expression values (z-score) of 6179 transcripts (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024351#pone.0024351.s007" target="_blank">Data S1</a>) regulated at any timepoint or in iPS/ES cells with respect to HFF1 cells (p_adj<0.05; fold change >1.5) are shown. …”

Sensitivity analysis of the model parameters. by Roswitha Dolcemascolo (12511789)

“…<p>Plots of mean and noise of expression as a function of IPTG, where solid lines correspond to the dynamics predicted with the adjusted parameter, dotted lines to the dynamics if the parameter increases 2-fold, and dashed lines to the dynamics if the parameter decreases 2-fold.…”

Modulation by decitabine of gene expression and growth of osteosarcoma U2OS cells and in xenografts: Identification of apoptotic genes as targets for demethylation-1 by Khaldoun Al-Romaih (79731)

“…</p><p></p>ice (panel B) using immunohistochemical staining with 5-mc-Ab. To the right a 20X enlargement of representative U2OS histology is shown. …”

Knockdown of <i>Adamts19</i> in XX gonads and <i>Ctrb1</i> in XY gonads. by Kathryn S. McClelland (687254)

“…Knockdown of ADAMTS19 in the XX gonad (n = 7, 8, 5, 5) showed no change in female somatic markers <i>Fst</i> (B) and <i>Irx3</i> (C) and a slight decrease in expression of germ cell marker <i>Ddx4</i> (D). …”

Multiplex Detection of Homo- and Heterodimerization of G Protein-Coupled Receptors by Proximity Biotinylation by Elisabeth Steel (545397)

“…As a test case for our newly developed assay, we have characterized the homo-dimerization of chemokine receptor CXCR4 and heterodimerization of CXCR4 with CCR2 or CCR5. …”

<b>Attenuation of an original novel goose parvovirus strain NMG21 via serial cell passage</b> by Dalin He (13763531)

“…Increased virus <a href="" target="_blank">titer</a> was observed at the 5th passage (P5). …”

Blood pressure effects of ephedrine treatment. by Daniel Radiloff (588253)

“…Tissue hypoxia was measured by pO₂ needle electrode tracings during inspired normoxia (1) and hypoxia at baseline (2), before (3) and after injection under normoxia (4), and during post-injection hypoxia (5). D: under post-treatment normoxia (panel D time point #4), ephedrine alone and in combination with ambrisentan significantly increased muscle oxygenation, compared to pre-treatment pO₂ (one-way ANOVA with Bonferroni correction, N = 4–8, p<0.05). …”

The combination of discontinuous dexamethasone and PEGylated asparaginase shows synergistic efficacy in bone marrow. by Seth E. Karol (780961)

The thermo-mechanical response of PP nanocomposites at high graphene loading by Kai Yang (73590)

Protein Tyrosine Phosphatase PTP1B Is Involved in Hippocampal Synapse Formation and Learning by Federico Fuentes (149005)

“…Notably, levels of ß-catenin-Tyr-654 phosphorylation increased ∼5-fold in the hippocampus of adult PTP1B^−/− (KO) mice compared to wild type (WT) mice and this was accompanied by a reduction in the amount of ß-catenin associated with N-cadherin. …”

Intact Polar Lipids. by B. Jacob Kendrick (662898)

“…Chloroplast lipids such as MGDG (yellow slices), DGDG (blue slices), and SQDG (pink slices) decrease dramatically in 18V as photosynthetic efficiency decreases. 18V also demonstrates a significant decrease in diacylglycerylcarboxy-N-hydroxymethyl-choline (DGCC, dark green slices) which is involved in fatty acid transport into the MGDG synthesis pathway. …”

<i>C6ST</i>-1 mRNA or 6-sulphated GAGs were not expressed in <i>C6ST</i>-1 KO mice. by Rachel Lin (215087)

“…The amplification of housekeeping Hprt acts as a positive control. (b) FACE gel showed a decrease of 6-sulphated GAGs in <i>C6ST</i>-1 KO animals compared to WT mice (lanes marked with “−”). …”

Cytosolic pH changes in palisade mesophyll cells of Gesneriaceae plants. by Noriaki Kadohama (382080)

“…<p>Cytosolic pH changes in palisade mesophyll cell of sensitive species (<i>Columnea</i> sp. and <i>Kohleria warszewiczii</i>) and insensitive species (<i>Sinningia speciosa</i> and <i>Streptocarpus</i> sp.) induced by a rapid temperature decrease. (A) Palisade mesophyll cells of <i>Columnea</i> sp. and <i>Kohleria warszewiczii</i> stained with pH-sensitive fluorescent dye, BCECF-AM. …”

Enhanced proteoglycan accumulation in articular cartilage of CCN2 transgenic mice. by Shinsuke Itoh (125939)

“…The content of TB metachromasia-positive proteoglycans decreased with aging; however, TG articular cartilage showed a greater accumulation of proteoglycans than did the cartilage of WT littermates at all time points. …”

Data_Sheet_1_Biochemical Composition and Energy Strategy Along the Reproductive Cycle of Female Octopus vulgaris in Galician Waters (NW Spain).PDF by Pilar Sieiro (9122633)

“…Additionally, the most abundant fatty acids (FA) in all tissues were 16:0, 18:0, 20:1n9, 20:4n6 (ARA), 20:5n3 (EPA) and 22:6n3 (DHA), with a clear predominance of long-chain polyunsaturated FA. …”