Journal: Journal of visualized experiments : JoVE

Article Title: Defining Gene Functions in Tumorigenesis by Ex Vivo Ablation of Floxed Alleles in Malignant Peripheral Nerve Sheath Tumor Cells

doi: 10.3791/62740

Figure Lengend Snippet: Table of Materials

Article Snippet: For the bioluminescence (MTT) assays, perform the assay exactly as outlined in the manufacturer’s instructions every 24 h for 72 h using a luminometer plate reader. table ft1 table-wrap mode="anchored" t5 caption a7 Name of Material/ Equipment Company Catalog Number Comments Ad5CMV-eGFP Gene Transfer Vector Core, Univ of Iowa VVC-U of Iowa-4 Ad5CMVCre-eGFP Gene Transfer Vector Core, Univ of Iowa VVC-U of Iowa-1174 alexa 568 secondary antibody Thermo/Fisher GαR A11036 Bioconductor Open Source Software for Bioninformatics Bioconductor http://www.bioconductor.org alternative statistical analysis tool used for step 4.4 CD31 Abcam ab28364 Celigo Image Cytometer Nexcelom Bioscience N/A Cell Stripper Corning 25-056-Cl mixture of chelators DAB staining kit Vector Labs MP-7800 DAVID ( D atabase for A nnotation, V isualization, and I ntegrated D iscovery) DAVID https://david.ncifcrf.gov functional enrichment analysis software used for step 4.5 DMEM Corning 15-013-Cl DreamTaq and Buffer (Genotyping PCR) Thermo/Fisher EP0701 and K1072 erbB4 antibodies Santa Cruz sc-284 erbB4 antibodies Abcam ab35374 erbB4 antibodies Millipore HFR1: 05-1133 FACS Sorter BD Biosciences Aria II Forskolin Sigma F6886 GenomeSpace Tools and Data Sources GenomeSpace https://genomespace.org/support/tools/ general resource for several types of open source bioinformatic tools for step 4.5 Glutamine Corning 25-005-Cl Gorilla G ene Ontology en RI chment ana L ysis and visua L iz A tion tool Gorilla N/A, http://cbl-gorilla.cs.technion.ac.il functional enrichment analysis software used for step 4.5 GSEA Gene Set Enrichment Analysis Broad Institute N/A, https://www.gsea-msigdb.org/gsea/index.jsp functional enrichment analysis software used for step 4.5 HSD: Athymic Nude-FOxn1nu mice Envigo (Previously Harlan Labs) 69 Illumina HiSeq2500 (next generation DNA sequencer) Illumina Hi Seq 2500 DNA sequencer used for step 4.2 Lasergene: ArrayStar Gene expression and variant analysis DNAStar LaserGene software N/A software statistical and normalization analysis used for step 4.4 Lasergene: SeqMan NGen sequence alignment assembly software alignment used for step 4.3 N/A software alignment used for step 4.3 Matrigel, low growth factor basement membrane matrix Corning 354230 NRG1-beta In house Generated by SLC, also commercially available from R & D Systems(396-HB-050/CF).

Techniques: Plasmid Preparation, Software, Cytometry, Staining, Functional Assay, Expressing, Variant Assay, Sequencing, Generated, Viability Assay, Amplification

Journal: Journal of chromatography. A

Article Title: Automating Data Analysis for Two-Dimensional Gas Chromatography/Time-of-Flight Mass Spectrometry Non-Targeted Analysis of Comparative Samples

doi: 10.1016/j.chroma.2018.02.016

Figure Lengend Snippet: The manual workflow used to select candidate analytes from a given GC×GC/ToF-MS data output analysis from the LECO® ChromaTOF® software’s Statistical Compare feature. This process can take several hours per sample, depending on the complexity of the sample.

Article Snippet: Using datasets from the soil extracts pre- and post-bioremediation, OCTpy selected, on average, 18% of the initial suggested analytes generated by the LECO ® ChromaTOF ® software Statistical Compare feature.

Techniques:

Journal: Journal of chromatography. A

Article Title: Automating Data Analysis for Two-Dimensional Gas Chromatography/Time-of-Flight Mass Spectrometry Non-Targeted Analysis of Comparative Samples

doi: 10.1016/j.chroma.2018.02.016

Figure Lengend Snippet: The automated workflow used to select candidate analytes from a given GC×GC/ToF-MS data output analysis from the LECO® ChromaTOF® software’s Statistical Compare feature. This process only take several minutes per sample, depending on the complexity of the sample.

Article Snippet: Using datasets from the soil extracts pre- and post-bioremediation, OCTpy selected, on average, 18% of the initial suggested analytes generated by the LECO ® ChromaTOF ® software Statistical Compare feature.

Techniques:

Journal: Journal of chromatography. A

Article Title: Automating Data Analysis for Two-Dimensional Gas Chromatography/Time-of-Flight Mass Spectrometry Non-Targeted Analysis of Comparative Samples

doi: 10.1016/j.chroma.2018.02.016

Figure Lengend Snippet: Manuals vs. Automated Result Comparisons Comparisons of candidate analytes selected by either manual analysis or OCTpy from the the LECO ® ChromaTOF ® software’s Statistical Compare (SC) feature list. Percent match between manual analysis and OCTpy was calculated based on the percent of the ratio between the number of candidate analytes that were selected in both OCTpy and manual analysis. For example, in fraction D, although OCTpy selected 20 candidate analytes, the 7 candidate analytes selected from manual analysis were also included in the OCTpy candidate analytes list, which resulted in 100% match.

Article Snippet: Using datasets from the soil extracts pre- and post-bioremediation, OCTpy selected, on average, 18% of the initial suggested analytes generated by the LECO ® ChromaTOF ® software Statistical Compare feature.

Techniques: Software