Journal:

Article Title: The impact of next-generation sequencing on genomics

doi: 10.1016/j.jgg.2011.02.003

Figure Lengend Snippet: The end-user software packages and cloud computing software for NGS data analysis.

Article Snippet: Although commercial end-user packages tend to carry a hefty price, some are available free online as detailed in . table ft1 table-wrap mode="anchored" t5 caption a7 Software packages Function Website End-user software packages Genomic workbench/CLCbio Multi-task http://www.clcbio.com/index.php?id=1331 NextGENe/SoftGenetics Multi-task http://softgenetics.com/NextGENe.html Genomatix Genome Analyzer Multi-task http://www.genomatix.de/genome_analyzer.html Zoom Multi-task http://www.bioinformaticssolutions.com/products/zoom/index.php SeqMan Ngen/DNASTAR Multi-task http://www.dnastar.com/t-products-seqman-ngen.aspx JMP Genomics Multi-task http://www.jmp.com/software/genomics/index.shtml RTG/Real Time Genomics Multi-task http://www.realtimegenomics.com/RTG-Software PASS Multi-task http://pass.cribi.unipd.it/cgi-bin/pass.pl?action=Download CASAVA Multi-task http://www.illumina.com/software/ Geneus/GenoLogics Multi-task http://www.genologics.com/solutions/research-informatics/ Roche Analysis tools Multi-task http://454.com/products-solutions/analysis-tools/index.asp VSRAP Multi-task http://sourceforge.net/apps/mediawiki/vancouvershortr/ BING Multi-task http://www.dinulab.org/bing PaCGeE/PGI Multi-task http://personalgenomicsinstitute.org/index.php/ GATK Multi-task http://www.broadinstitute.org/gsa/wiki/index.php/ Geneious Pro Multi-task http://www.geneious.com/default,1246,NGS%20Assembly.sm Partek GS/Partek Multi-task http://www.partek.com/partekgs Bioscope Multi-task https://products.appliedbiosystems.com/ab/en/US/adirect/ Cloud computing Crossbow Mapping and SNP calling http://bowtie-bio.sf.net CloudBurst Reference-based mapping http://sourceforge.net/apps/mediawiki/cloudburst-bio/ Contrail De novo assembly http://sourceforge.net/apps/mediawiki/contrail-bio/ Cloud-MAQ Modified-Maq for cloud http://geschickten.com/download.html Bioscope Reference-based mapping https://products.appliedbiosystems.com/ab/en/US/adirect/ Cycle Computing Cloud computing http://www.cyclecomputing.com/ GenomeQuest Customer service http://www.genomequest.com/ Geospiza/GeneSifter Customer service http://www.geospiza.com/Contact/genesiftertrial_ng.shtml Open in a separate window The end-user software packages and cloud computing software for NGS data analysis.

Techniques: Software, Modification

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, Gene Expression, Variant Assay, Sequencing, Membrane, Generated, Viability Assay, Amplification

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