Journal: bioRxiv

Article Title: Identification Drug Targets for Oxaliplatin-Induced Cardiotoxicity without Affecting Cancer Treatment through Inter Variability Cross-Correlation Analysis (IVCCA)

doi: 10.1101/2024.02.11.579390

Figure Lengend Snippet: Data is processed through a traditional pipeline of RNA-seq data preprocessing and differential expression genes (DEGs) extraction using specific filter parameters such as False Discovery Rate (FDR) <0.05 and fold change (FC) >1.5. The data are utilized to construct a correlation matrix, its correlation heatmap is generated to visualize DEGs’ correlation distribution. For further analysis, the absolute values of the correlations are ordered. The sorted heatmap aids in the visualization of the top genes. Clustering is performed using Dendrogram, Principal Component Analysis (PCA), and t-distributed Stochastic Neighbor Embedding (t-SNE) methods, followed by distance thresholding (for the Dendrogram results) or K-means (for the PCA and t-SNE results) for finer clustering. Clusters were analyzed via STRING or network analysis to identify potential target genes. All pathways, including generated and existing ones from databases like GO and KEGG, are quantitatively compared using novel indices and ranked for relevance.

Article Snippet: Our implemented t-distributed Stochastic Neighbor Embedding (t-SNE) toolbox that performs t-SNE calculations ( ) uses the results from the correlation matrix and presents the genes based on their correlation values in 3D using a built-in ‘ tsne ’ function implemented in MATLAB.

Techniques: RNA Sequencing Assay, Expressing, Extraction, Construct, Generated

Journal: Cell

Article Title: Cerebellar neurodynamics predict decision timing and outcome on single-trial level

doi: 10.1016/j.cell.2019.12.018

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Tg( elavl3:H2B-GCaMP6s ) ( Vladimirov et al., 2014 ) N/A Tg(gSA2AzGFF152B) ( Takeuchi et al., 2015 ) N/A Tg(Huc:H2B-GCaMP6s; GAD1b:RFP) ( Freeman et al., 2014 ; Satou et al, 2013 ) N/A Tg(UAS:GCaMP6s) ( Filosa et al, 2016 ) N/A Software and Algorithms μManager Open Imaging https://micro-manager.org/ MATLAB (Behavioral and imaging analysis, modeling) MathWorks https://www.mathworks.com/products/matlab.html FIJI (ImageJ) (Image Processing) NIH http://fiji.sc Custom data-processing pipeline for LFM data ( Prevedel et al, 2014 ) https://static-content.springer.com/esm/art%3A10.1038%2Fnmeth.2964/MediaObjects/41592_2014_BFnmeth2964_MOESM189_ESM.zip Demixed Principal Component Analysis (dPCA) ( Kobak et al, 2016 ) https://github.com/machenslab/dPCA t-Distributed Stochastic Neighbor Embedding (t-SNE) ( Maaten and Hinton, 2008 ) https://lvdmaaten.github.io/tsne/ Independent Component Analysis (FastICA) ( Hyvarinen and Oja, 2000 ) https://research.ics.aalto.fi/ica/fastica/ Scanlmage ( Pologruto et al, 2003 ) http://scanimage.vidriotechnologies.com/display/SIH/ScanImage+Home CalmAn-MATLAB ( Giovannucci et al, 2019 ) https://github.com/flatironinstitute/CaImAn-MATLAB DeepLabCut 2.0 ( Nath et al, 2019 ) https://github.com/AlexEMG/DeepLabCut Open in a separate window KEY RESOURCES TABLE Whole-brain Ca 2+ imaging and decision making in larval zebrafish on the single-trial level Pre-motor bifurcation and trial-by-trial changes of functional connectivity Cerebellar activity predicts decision outcome and decision time >10 s before movement Hemisphere difference encodes decision; joint hemisphere activity encodes timing

Techniques: Software, Imaging

Journal: Neuron

Article Title: Assemblies of Perisomatic GABAergic Neurons in the Developing Barrel Cortex

doi: 10.1016/j.neuron.2019.10.007

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-GABA Sigma-Aldrich Cat#: A2052; RRID:AB_477652 Guinea pig polyclonal anti-GAD2 Synaptic Systems Cat#: 198104; RRID: AB_10557995 Guinea pig polyclonal anti-VGluT2 Merck Millipore Cat#: AB2251-I; RRID:AB_2665454 Mouse monoclonal anti-Syt2 Developmental Studies Hybridoma Bank Cat#: A2315626; RRID: AB_2315226 Bacterial and Virus Strains AAV1.syn.GCaMP6s.WPRE.SV40 UPenn viral core Cat#: 100843 Experimental Models: Organisms/Strains Swiss Webster (CFW) C.E Janvier SW-F/ SW-M Gad67.Cre a gift from H. Monyer Heidelberg University N/A RCL-GCaMP6s (Ai96) Jackson Laboratories 02 4106 SST.Cre a gift from N. Heintz, Rockefeller University N/A Lhx6.Cre Jackson Laboratories 026555 5HT3aR.Cre a gift from N. Heintz, Rockefeller University N/A GAD67-GFP-KI a gift from K. Obata Department of Morphological Brain Science, Kyoto N/A 5-HT3aR-GFP-KI a gift from G. Fishell Harvard University N/A Software and Algorithms CaImAn Pnevmatikakis et al., 2016 ; Giovannucci et al., 2018 https://github.com/flatironinstitute/CaImAn-MATLAB NoRMCorre Pnevmatikakis and Giovannucci, 2017 https://github.com/flatironinstitute/NoRMCorre Iterative K-means clustering Malvache et al., 2016 http://gitlab.com/cossartlab t-SNE Van Der Maaten and Hinton, 2008 https://lvdmaaten.github.io/tsne/#implementations Open in a separate window KEY RESOURCES TABLE In the developing barrel cortex, GABAergic neurons form functional assemblies Prospective parvalbumin interneurons segregate into spatially clustered assemblies Somatostatin interneurons display broadly correlated firing GABA assemblies are regulated by sensory inputs

Techniques: Virus, Software