Journal: Neuron

Article Title: The Epigenetic State of PRDM16-regulated Enhancers in Radial Glia Controls Cortical Neuron Position

doi: 10.1016/j.neuron.2018.04.033

Figure Lengend Snippet: RNA sequencing

Article Snippet: Forward: 5′-AAAAAGCAGTTGGCACAAGA-3′ Reverse: 5′-GGTCTATCATGGGCTGCACT-3′ This paper N/A Fluorescent in situ hybridization RNAscope probe Mm Pdzrn3 Advanced Cell Diagnostics Cat #517061 RNAscope probe Mm Itga6 Advanced Cell Diagnostics Cat #441701 RNAscope probe Mm Gabra2 Advanced Cell Diagnostics Cat #435011 RNAscope probe Mm Tubb3 Advanced Cell Diagnostics Cat #423391 Recombinant DNA pCAG-TAG Addgene Plasmid #26771 CAG-GFP-IRES-CRE Addgene Plasmid #48201 pCAGIG Addgene Plasmid #11159 pCMV-VSV-G Addgene Plasmid #8454 Hes5-Luc Addgene Plasmid #41724 pcDNA3.1 Prdm16 Addgene Plasmid #15503 pCAG- Prdm16 -IRES- GFP This paper N/A Hes5p- Prdm16 -IRES- GFP This paper N/A Hes5p- ΔPRdm16 -IRES- GFP This paper N/A pCAGIG Pdzrn3 This paper N/A Software and Algorithms ImageJ/ Fiji 1.49S Wayne Rasband National Institutes of Health, U.S.A. https://imagej.nih.gov/ij/ Imaris 7.0 Bitplane http://www.bitplane.com/releasenotes/imaris700.aspx Integrative Genomics Viewer (IGV) 2.3 Broad Institute MIT/Harvard http://software.broadinstitute.org/software/igv/ MATLAB R2017b MathWorks https://www.mathworks.com/products/matlab.html Cutadapt (Martin, 2011) http://code.google.com/p/cutadapt/ STAR (Dobin et al., 2013) http://code.google.com/p/rna-star/ FeatureCounts (Liao et al., 2014) http://subread.sourceforge.net DESeq2 (Love et al., 2014) http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html gProfiler (Reimand et al., 2007) http://biit.cs.ut.ee/gprofiler/ REVIGO (Supek et al., 2011) http://revigo.irb.hr/ Bowtie2 2.2.8 (Langmead et al., 2009) http://bowtie.cbcb.umd.edu MACS2 2.1.1 (Zhang et al., 2008) https://pypi.python.org/pypi/MACS2 IDR R package (Li et al., 2011) http://cran.rproject.org/web/packages/idr/index.html HOMER v4.6 suite (Heinz et al., 2010) http://homer.ucsd.edu/homer/ DeepTools2 (Ramírez et al., 2016) deeptools.iefreiburg.mpg.de BETA v1.0.7 ( Wang et al., 2013 ) http://cistrome.org/BETA/ Open in a separate window RNA sequencing Chromatin immunoprecipitation and sequencing Approximately 20–40 million cortical cells were dual crosslinked by incubating in 1.5 mM EGS (ethylene glycol bis[succinimidyl succinate]) solution (Thermo Scientific) for 20 min at RT with rotation and then 1% PFA plus 1.5 mM EGS for an additional 10 min at RT.

Techniques: Virus, Recombinant, Blocking Assay, Nucleic Acid Hybridization, Isolation, Imaging, In Situ Hybridization, shRNA, Control, Real-time Polymerase Chain Reaction, RNAscope, Plasmid Preparation, Software