A Novel Bayesian Outlier Score Based on the Negative Binomial Distribution for Detecting Aberrantly Expressed Genes in RNA-Seq Gene Expression Count Data by Edin Salkovic (16891479)

Subjects:

RNA-seq Reveals Dysregulation of Novel Melanocyte Genes upon Oxidative Stress: Implications in Vitiligo Pathogenesis by Konduru Seetharama Sastry (14603308)

“…Quantitative PCR and western blot analysis of selected proteins, performed on PIG1 and primary human epidermal melanocytes, confirmed the RNA-seq data. …”

Integrated Transcriptome and Pathway Analyses Revealed Multiple Activated Pathways in Breast Cancer by Radhakrishnan Vishnubalaji (3563306)

“…A selected number of genes from the RNA-Seq analysis were subsequently validated using qRT-PCR. …”

iPSC-Derived Pancreatic Progenitors Lacking FOXA2 Reveal Alterations in miRNA Expression Targeting Key Pancreatic Genes by Noura Aldous (15429873)

“…Furthermore, genes associated with MODY, pancreatic development, Notch and WNT signaling pathways were downregulated, while glucose and cholesterol homeostasis associated genes were upregulated. miRNA-seq data analysis on FOXA2–/–PPs showed 107 downregulated (Log2 FC < −1.0, p < 0.05) and 111 upregulated (Log2 FC > 1.0, p < 0.05) differentially expressed miRNAs. …”

iPSC-Derived Pancreatic Progenitors Lacking FOXA2 Reveal Alterations in miRNA Expression Targeting Key Pancreatic Genes by Noura Aldous (15429873)

Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA) by Julien Richard Albert (655437)

Immunoprofile of childhood diabetes by Meritxell Espino-Guarch (15430868)

Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of blood by Mahesh Kumar Reddy Kalikiri (17886695)

Subjects:

Comparative Analysis of Preterm and Full-term Births using Transcriptomic Profiling by Amal E. I. Ahmed (22789562)

Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer by Hibah Shaath (5599658)

“…Additionally, potential interaction between differentially expressed lncRNAs such as H19, SNHG5, and GATA2-AS1 with multiple miRNAs has been revealed. Taken together, our data provides thorough analysis of dysregulated protein-coding and non-coding RNAs in CRC highlighting numerous associations and regulatory networks thus providing better understanding of CRC.…”

Computational identification of genetic subnetwork modules associated with maize defense response to Fusarium verticillioides by Mansuck Kim (19570903)

“…We obtained time-course RNA-seq data from B73 maize inoculated with wild type F. verticillioides and a loss-of-virulence mutant, and subsequently established a computational pipeline for network-based comparative analysis. …”

Computational and Transcriptome Analyses Revealed Preferential Induction of Chemotaxis and Lipid Synthesis by SARS-CoV-2 by Hibah Shaath (5599658)

“…In this study, we analyzed RNA-seq transcriptome data from Calu-3 human lung epithelial cells infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compared to five other viruses namely, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East Respiratory Syndrome (SARS-MERS), influenzavirus A (FLUA), influenzavirus B (FLUB), and rhinovirus (RHINO) compared to mock-infected cells and characterized their coding and noncoding RNA transcriptional portraits. …”

A multi-omics approach reveals dysregulated TNF-related signaling pathways in circulating NK and T cell subsets of young children with autism by Wared Nour-Eldine (13904298)

“…Using a multimodal approach, we integrated transcriptomic, proteomic, and single-cell RNA-seq data analyses from this cohort. Targeted transcriptomic profiling identified differential expression of 50 immune-related genes in the circulating PBMCs of children with ASD, three of which (JAK3, CUL2, and CARD11) negatively correlated with ASD symptom severity. …”

PD-L1 Blockade by Atezolizumab Downregulates Signaling Pathways Associated with Tumor Growth, Metastasis, and Hypoxia in Human Triple Negative Breast Cancer by Reem Saleh (3513056)

“…The expression of selected genes, from RNA-Seq data, was subsequently validated using RT-qPCR in the MDA-MB-231 and MDA-MB-468 TNBC cells following atezolizumab treatment. …”

Transcriptomic Analyses Revealed Systemic Alterations in Gene Expression in Circulation and Tumor Microenvironment of Colorectal Cancer Patients by Hibah Shaath (5599658)

“…The expression of selected immune-related genes from the RNA-Seq data were further validated using qRT-PCR. …”

Therapeutic targeting of the TPX2/TTK network in colorectal cancer by Hibah Shaath (5599658)

“…</p><h3>Methods</h3><p dir="ltr">RNA-Seq was conducted using the illumina platform, while bioinformatics analyses were conducted using CLC genomics workbench and iDEP.951. …”

Transcriptional alterations of protein coding and noncoding RNAs in triple negative breast cancer in response to DNA methyltransferases inhibition by Ramesh Elango (7542068)

“…</p><h3>Conclusions</h3><p dir="ltr">Taken together, our data provides a comprehensive view of transcriptome alterations in the coding and noncoding transcriptome in TNBC in response to DNMT inhibition.…”