Journal: Journal of Experimental Botany

Article Title: A comparison of the low temperature transcriptomes and CBF regulons of three plant species that differ in freezing tolerance: Solanum commersonii , Solanum tuberosum , and Arabidopsis thaliana

doi: 10.1093/jxb/err066

Figure Lengend Snippet: Comparison of cold- and CBF-regulated pOGs of S. tuberosum (St), S. commersonii (Sc), and A. thaliana (At). (A) A total of 8714 putative orthologous groups (pOGs) were identified between At and St. The Venn diagram shows pOGs with at least one At gene on the ATH1 chip, at least one potato clone on the potato cDNA array, or at least one gene from each species in both arrays (overlap). (B) Overlaps of cold-induced and cold-repressed pOGs in Sc, St, and At are shown from the pOGs present in both arrays in A. (C) Comparison of CBF regulon pOGs in Sc, St, and At. Overlaps of CBF-induced and CBF-repressed pOGs are shown based on the pOGs present in both arrays.

Article Snippet: A list of cold-regulated A. thaliana genes was generated from a large number of previously published microarray experiments ( Vogel et al. , 2005 ; Kilian et al. , 2007 ) and new experiments (unpublished arrays have been submitted to Array Express) that used the Affymetrix ATH1 gene chip to monitor transcript levels ( Supplementary Table S2 at JXB online).

Techniques:

Journal: PLoS Computational Biology

Article Title: Computational Predictions Provide Insights into the Biology of TAL Effector Target Sites

doi: 10.1371/journal.pcbi.1002962

Figure Lengend Snippet: We consider as performance measures the number of predicted targets consistent with up-regulation in gene expression microarrays for different rank cutoffs and thresholds of 1 and 0.5 on the log-fold changes (left panel), and the precision-recall (PR) curve (right panel) using a threshold of 1 on the log-fold changes.

Article Snippet: The expression levels of A. thaliana genes are measured by Affymetrix Ath1 microarrays (imaGenes GmbH, Berlin, Germany), RMA normalized, and fold changes are determined for each of the 3 transgenic lines compared to 3 non-transgenic lines independently.

Techniques: Expressing

Journal: PLoS ONE

Article Title: GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences

doi: 10.1371/journal.pone.0025279

Figure Lengend Snippet: ( A ) Comparison of estimated log 2 -fold changes from analysis of microarrays (x-axis) and RNA-Seq using GENE-counter running NBPSeq (y-axis). Only induced genes measurable by both platforms are presented. Differentially induced genes are colored to highlight genes uniquely identified using microarrays (open red down triangles) or RNA-Seq (open blue up triangles) and found common between the two methods (purple crosses). ( B ) Three-way Venn comparing differentially expressed genes identified from GENE-counter's assessment of RNA-Seq data and analysis of microarrays. Only genes measurable using both methods were included in the comparison.

Article Snippet: The mRNA labeling, hybridization, and scanning of Affymetrix ATH1 microarrays were done by the CGRB core facility at OSU.

Techniques: Comparison, RNA Sequencing

Journal: Bioengineered

Article Title: Small activating RNA activation of ATOH1 promotes regeneration of human inner ear hair cells.

doi: 10.1080/21655979.2022.2045835

Figure Lengend Snippet: Figure 2. Screening of ATOH1 small activating RNAs in 293 T cells and mesenchymal stem cells. Cells were transfected with the indicated small activating RNAs using RNAiMAX at the indicated concentrations for 72 h. Mock samples were transfected in the absence of duplex RNA. Plasmid DNA was transfected at 1 µg/µl using Lipofectamine 3000. The transfected cells were subjected to RT–qPCR after RNA isolation, an RT reaction to generate cDNA and a Western blotting assay after protein isolation. A and B. Relative mRNA expression levels of the ATOH1 gene in 293 T cells (a) and mesenchymal stem cells (b) 72 h after transfection. C and D. ATOH1 protein levels assessed by Western blotting in 293 T cells (c) and mesenchymal stem cells (d) at 72 h after transfection. E and F. Relative ATOH1 mRNA expression levels in response to different small activating RNA concentrations.

Article Snippet: Induction of hair cell-like cells The induced hair cell progenitor cells were maintained in 6-well plates (2 × 105 cells per well) and in a mixed medium consisting of serum-free DMEM/F12 and N2/B27 and were transfected with ATOH1 small activating RNAs using RNAiMAX or an ATOH1 plasmid (ORIGENE, #RC210192) using Lipofectamine 3000 for 10 days.

Techniques: Transfection, Plasmid Preparation, Quantitative RT-PCR, Isolation, Western Blot, Expressing