Journal: Progress in Earth and Planetary Science

Article Title: Deformation mechanisms and fluid conditions of mélange shear zones associated with seamount subduction

doi: 10.1186/s40645-024-00641-y

Figure Lengend Snippet: Fig. 5 Micritic limestone lenses in the BLM. Panels b–e were generated using MTEX software (Hielscher and Schaeben 2008; Mainprice et al. 2014). a Microcrystalline calcite (Cc) with radiolarian tests showing partial recrystallization to calcite. b Histogram of microcrystalline calcite grain size calculated from the diameter of reconstructed EBSD grains. c Histogram of grain orientation spread (GOS) of calcite, showing a low degree of intragranular misorientation. d GOS map of calcite on EBSD band contrast image of the micritic limestone. A given pixel within each of the calcite grains is colored by the angular degree of intragranular misorientation relative to the mean orientation of the parent grain. Most white grains correspond to chlorite and albite grains, identified by EBSD indexing and optical microscopy. Unindexed pixels are black. e CPO pole figures of microcrystalline calcite grains. CPO is plotted as equal-area, upper hemisphere projections. The crystal directions shown here were selected to examine the possibility of deformation under low-temperature calcite slip systems (De Bresser and Spiers 1997). The M-index (m) indicates that the fabric intensity is very weak (Skemer et al. 2005). Grains are plotted with the X-direction parallel to lineation and the Z-direction normal to foliation. N represents the number of measured points. f Micritic limestone (Cc) and basalt lenses in green chloritic matrix with S–C fabric showing top-to-SE shear sense. Dark seams contain Fe and Ti oxide minerals

Article Snippet: Quantitative analyses of EBSD data, including map analyses (e.g., grain reconstruction, grain size, and misorientation), CPO pole figures, and orientation distribution functions (e.g., M-index), were carried out using the MTEX toolbox for MATLAB (Hielscher and Schaeben 2008; Mainprice et al. 2014).

Techniques: Generated, Software, Recrystallization, Microscopy, Shear

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

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