Distribution of Recessive Genetic Defect Carriers in Holstein Friesian Cattle: A Polish Perspective by Marta Gozdek, Sebastian Mucha, Adam Prostek, Dariusz Kamola, Tomasz Sadkowski

“…The studies were performed using Illumina Infinium microarrays. Among both bulls and cows, the highest numbers of carriers were detected for HH5 (appropriately 6.7% and 5.4%). …”
Get full text

Imputation of variants from the 1000 Genomes Project modestly improves known associations and can identify low-frequency variant-phenotype associations undetected by HapMap based i... by Andrew R Wood, John R B Perry, Toshiko Tanaka, Dena G Hernandez, Hou-Feng Zheng, David Melzer, J Raphael Gibbs, Michael A Nalls, Michael N Weedon, Tim D Spector, J Brent Richards, Stefania Bandinelli, Luigi Ferrucci, Andrew B Singleton, Timothy M Frayling

“…Genome-wide association (GWA) studies have been limited by the reliance on common variants present on microarrays or imputable from the HapMap Project data. …”
Get full text

Multi-institutional TSA-amplified Multiplexed Immunofluorescence Reproducibility Evaluation (MITRE) Study by Bernard A Fox, Chichung Wang, Kristin Roman, Carla Coltharp, Carmen Ballesteros-Merino, Shawn M Jensen, Janis M Taube, David L Rimm, Cliff Hoyt, Mei Jiang, Edwin R Parra, Ignacio Wistuba, Elizabeth L Engle, John McGuire, Bethany Remeniuk, Darren Locke

“…Serial sections from tonsil and breast carcinoma and non-small cell lung cancer (NSCLC) tissue microarrays (TMAs), TSA-Opal fluorescent detection reagents, and antibodies were distributed to the six sites equipped with a Leica Bond Rx autostainer and a Vectra Polaris multispectral imaging platform. …”
Get full text

Serum LncRNAs Profiles Serve as Novel Potential Biomarkers for the Diagnosis of HBV-Positive Hepatocellular Carcinoma. by Kang Wang, Wei Xing Guo, Nan Li, Chun Fang Gao, Jie Shi, Yu Fu Tang, Feng Shen, Meng Chao Wu, Shan Rong Liu, Shu Qun Cheng

“…<h4>Methods</h4>lncRNA microarrays were utilized to measure the differential expression of lncRNAs between tumor tissues and corresponding non-tumor tissues in HBV-positive hapatocellular carcinoma. uc001ncr and AX800134 were selected as candidate lncRNAs and detected in three independent cohorts containing a total of 684 participants (healthy individuals and chronic HBV patients and HBV-positive HCC patients) who were recruited between March 2011 and December 2012. …”
Get full text

HERV-derived epitopes represent new targets for T-cell-based immunotherapies in ovarian cancer by Qing Wang, Maha Ayyoub, Olivia Le Saux, Paola Bonaventura, Isabelle Treilleux, Nicolas Chopin, Clarisse Dubois, Virginie Mutez, Nicolas Chuvin, Yann Estornes, Jenny Valladeau-Guilemond, Stephane Depil, Nicolas Gadot, Marie Michelas, Audrey Page, Olivier Tabone, Marie Delles, Sarah Moran, Thibault Richard, Marjorie Lacourrège, Dina M Tawfik, Ema Etchegaray, Adrian Valente, Rasha E Boulos, Gabriel Jimenez Dominguez

“…Human endogenous retroviruses (HERVs) are aberrantly expressed by tumor cells and may represent a source of shared T-cell epitopes for cancer immunotherapy regardless of the tumor mutational burden.Methods A transcriptomic analysis based on RNA sequencing was developed to quantify the expression of HERV-K sequences containing the selected epitopes. The presence of HERV-K/HML-2 Gag antigen was then assessed by immunohistochemistry (IHC) on tumor microarrays from ovarian cancer samples and normal ovarian tissues. …”
Get full text

MaGIC: a program to generate targeted marker sets for genome-wide association studies by Claire L. Simpson, Valerie K. Hansen, Pak C. Sham, Andrew Collins, John F. Powell, Ammar Al-Chalabi

“…High-throughput genotyping technologies such as DNA pooling and DNA microarrays mean that whole-genome screens are now practical for complex disease gene discovery using association studies. …”
Get full text

Identification of vascular and hematopoietic genes downstream of etsrp by deep sequencing in zebrafish. by Gustavo Gomez, Jae-Hyung Lee, Matthew B Veldman, Jing Lu, Xinshu Xiao, Shuo Lin

“…Expression studies of 50 selected candidate genes from this dataset resulted in the identification of 39 new genes that are expressed in vascular cells. …”
Get full text

The transcription factor SOX18 regulates the expression of matrix metalloproteinase 7 and guidance molecules in human endothelial cells. by Martina Hoeth, Heide Niederleithner, Renate Hofer-Warbinek, Martin Bilban, Herbert Mayer, Ulrike Resch, Christof Lemberger, Oswald Wagner, Erhard Hofer, Peter Petzelbauer, Rainer de Martin

“…<h4>Methodology/principal findings</h4>SOX18 was expressed in HUVEC using a recombinant adenoviral vector and the altered gene expression profile was analyzed using microarrays. Expression of several regulated candidate SOX18 target genes was verified by real-time PCR. …”
Get full text

Comprehensive analysis of microRNA expression profile in malignant glioma tissues by Monika Piwecka, Katarzyna Rolle, Agnieszka Belter, Anna Maria Barciszewska, Marek Żywicki, Marcin Michalak, Stanisław Nowak, Mirosława Z. Naskręt-Barciszewska, Jan Barciszewski

“…We investigated the global miRNA profile of malignant glioma tissues with miRNA microarrays, deep sequencing and meta‐analysis. We selected miRNAs that were most frequently deregulated in glioblastoma tissues, as well as in peritumoral areas, in comparison with normal human brain. …”
Get full text

Revealing new mouse epicardial cell markers through transcriptomics. by Lars Bochmann, Padmini Sarathchandra, Federica Mori, Enrique Lara-Pezzi, Domenico Lazzaro, Nadia Rosenthal

“…<h4>Methodology</h4>Using laser capture microscopy, we isolated the epicardial layer from the adult murine heart before or after cardiac infarction in wildtype mice and mice expressing a transgenic IGF-1 propeptide (mIGF-1) that enhances cardiac repair, and analyzed the transcription profile using DNA microarrays.<h4>Principal findings</h4>Expression of epithelial genes such as basonuclin, dermokine, and glycoprotein M6A are highly enriched in the epicardial layer, which maintains expression of selected embryonic genes involved in epicardial development in mIGF-1 transgenic hearts. …”
Get full text

Multi-Scale Genomic, Transcriptomic and Proteomic Analysis of Colorectal Cancer Cell Lines to Identify Novel Biomarkers. by Romina Briffa, Inhwa Um, Dana Faratian, Ying Zhou, Arran K Turnbull, Simon P Langdon, David J Harrison

“…Selecting colorectal cancer (CRC) patients likely to respond to therapy remains a clinical challenge. …”
Get full text

Nonlinear Quantitative Radiation Sensitivity Prediction Model Based on NCI-60 Cancer Cell Lines by Chunying Zhang, Luc Girard, Amit Das, Sun Chen, Guangqiang Zheng, Kai Song

“…Important radiation therapy (RT) related genes were selected by significance analysis of microarrays (SAM). …”
Get full text

Classification of gliomas based on genome-wide DNA methylation profiles and immunohistochemical analysis: a short study by Olga Taryma-Leśniak, Kamil Buczkowski, Tomasz Klepinowski, Maciej Jankowski, Szymon Retfiński, Bartłomiej Sagan, Leszek Sagan, Ewa Szutowicz, Kacper Winiarski, Marta Masztalewicz, Przemysław Nowacki, Marta Sobalska-Kwapis, Dominik Strapagiel, Wojciech Kloc, Beata Lipska-Ziętkiewicz, Ewa Iżycka-Świeszewska, Tomasz K. Wojdacz

“…The formalin-fixed paraffin-embedded (FFPE) and freshly frozen (FF) samples were analyzed using Infinium Methylation-EPIC microarrays. The diagnosis was changed in two cases, and two other cases were classified as control tissue due to the low content of neoplastic cells in examined frozen samples. …”
Get full text

Biomarker-Based Nomogram to Predict Neoadjuvant Chemotherapy Response in Muscle-Invasive Bladder Cancer by Meritxell Pérez, Juan José Lozano, Mercedes Ingelmo-Torres, Montserrat Domenech, Caterina Fernández Ramón, J. Alfred Witjes, Antoine G. van der Heijden, Maria José Requena, Antonio Coy, Ricard Calderon, Begoña Mellado, Antonio Alcaraz, Antoni Vilaseca, Maria J. Ribal

“…Gene expression patterns were analysed in 34 samples from transurethral resection of the bladder (TURB) using Illumina microarrays. The expression levels of 45 selected differentially expressed genes between responders and non-responders to NAC were validated by quantitative PCR in an independent cohort of 157 patients. …”
Get full text

The Impact of Antenatal and Postnatal Factors on the Development of the Pulmonary Microvasculature in Preterm Infants by Raluca Chirculescu, Ruxandra Viorica Stănculescu, Paul Cristian Bălănescu, Gheorghe Peltecu

“…<b>Methods</b>: The investigation analyzed 67 cases of preterm infants, whose lifespans ranged from 1 day to 149 days. After selecting the cases from the autopsy database, two lung tissue microarrays were created. …”
Get full text

Identification of components associated with thermal acclimation of photosystem II in Synechocystis sp. PCC6803. by John G Rowland, Xin Pang, Iwane Suzuki, Norio Murata, William J Simon, Antoni R Slabas

“…<h4>Methodology/findings</h4>We have analysed gene expression using whole-genome microarrays and monitored alterations in physiology during acclimation of PSII to elevated growth temperature in Synechocystis sp. …”
Get full text

Advanced strategies for screening and identifying RNA-targeted small molecules: Bridging therapeutic potential and innovation by Zukela Ruzi, Daxiong Han, Kailibinuer Aierken

“…However, their dynamic nature and structural complexity have historically posed challenges in developing small molecules with high affinity and selectivity. In recent years, significant advancements in screening methodologies, such as high-throughput screening (HTS), small molecule microarrays (SMMs), and DNA-encoded libraries (DELs), have facilitated the identification of RNA-binding small molecules with enhanced specificity. …”
Get full text

Distinct roles of non-canonical poly(A) polymerases in RNA metabolism. by Salvatore San Paolo, Stepanka Vanacova, Luca Schenk, Tanja Scherrer, Diana Blank, Walter Keller, André P Gerber

“…In conclusion, our results suggest that paralogous TRAMP complexes have distinct RNA selectivities with functional implications in RNA surveillance as well as other RNA-related processes. …”
Get full text

Interleukin-13 receptor alpha 2 expression in tumor cells is associated with reduced disease-free survival in patients with luminal subtype invasive breast cancer by Hee Jung Kwon, Jung Eun Choi, Young Kyung Bae

“…Interleukin-13 receptor alpha 2 expressions were assessed by immunohistochemistry in tissue microarrays of 1283 invasive breast cancer samples, and associations between these expressions and clinicopathological variables and clinical outcomes were investigated. …”
Get full text

In vitro methodologies to evaluate nanocarriers for cancer treatment: where are we? by Giovanna Cassone Salata, Camila Megumi Hirokawa, Giovanna Barros de Melo, Isabella Draszesski Malagó, Jessica Ribeiro Nunes, Julia Sapienza Passos, Regina Gomes Daré, Luciana B. Lopes

“…Abstract Cancer treatment continues to face significant challenges, including lack of selectivity, systemic toxicity, and the adaptive resistance mechanisms of cancer cells, which limit the effectiveness of conventional therapies. …”
Get full text