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s1.docx, s2.dox Xiang-Nan Jiang

Xiang-Nan Jiang, Bao-Hua Yu, Wei-Ge Wang, Xiao-Yan Zhou & Xiao-Qiu Li
Primers for the detection of ALK fusion transcripts and summary of immunohistochemical findings

s1.docx, s2.dox Xiang-Nan Jiang

Xiang-Nan Jiang, Bao-Hua Yu, Wei-Ge Wang, Xiao-Yan Zhou & Xiao-Qiu Li
Primers for the detection of ALK fusion transcripts and summary of immunohistochemical findings

The graph-tool python library

Tiago P. Peixoto
Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). Contrary to most other python modules with similar functionality, the core data structures and algorithms are implemented in C++, making extensive use of template metaprogramming, based heavily on the Boost Graph Library. This confers it a level of performance that is comparable (both in memory usage and computation time) to that of a pure C/C++ library.

TPLakes_Temperature

Wei Wan
The first comprehensive data set of 15-year (2001–2015) nighttime and daytime lake surface water temperature (LSWT) of 374 lakes (≥10 km2 each) over the Tibetan Plateau, using MODIS (Moderate Resolution Imaging Spectroradiometer) Land Surface Temperature (LST) products as well as four lake boundary shapefiles (i.e. 2002, 2005, 2009, and 2014) derived from Landsat/CBERS/GaoFen-1 satellite images.

TPLakes_Temperature

Wei Wan
The first comprehensive data set of 15-year (2001–2015) nighttime and daytime lake surface water temperature (LSWT) of 374 lakes (≥10 km2 each) over the Tibetan Plateau, using MODIS (Moderate Resolution Imaging Spectroradiometer) Land Surface Temperature (LST) products as well as four lake boundary shapefiles (i.e. 2002, 2005, 2009, and 2014) derived from Landsat/CBERS/GaoFen-1 satellite images.

Additional file 1: of Atp8 is in the ground pattern of flatworm mitochondrial genomes

Bernhard Egger, Lutz Bachmann & Bastian Fromm
Mitochondrial genome sequence from the assembled nuclear genome of Macrostomum lignano [11]. (TXT 14 kb)

Additional file 11: of Atp8 is in the ground pattern of flatworm mitochondrial genomes

Bernhard Egger, Lutz Bachmann & Bastian Fromm
atp8 alignment matrix with triclads (for details see Additional file 9). (TXT 4 kb)

Additional file 10: of Atp8 is in the ground pattern of flatworm mitochondrial genomes

Bernhard Egger, Lutz Bachmann & Bastian Fromm
atp8 alignment matrix without triclads (for details see Fig. 4). (TXT 1 kb)

Additional file 4: Tables S1 and S2. of Quantitative analysis of cryptic splicing associated with TDP-43 depletion

Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian Isaacs & Vincent Plagnol
Quantification of all results for each cryptic exon discovered by CryptEx in mouse (ST1) and human (ST2). Change in percent spliced in (∆PSI) scores were calculated by taking the difference of ratios of novel splice junctions over the sum of novel and annotated (intron-spanning) splice junctions in control and depletion samples for the 5′ and 3′ splice junctions. (ZIP 8 kb)

Additional file 1: Figure S1. of Quantitative analysis of cryptic splicing associated with TDP-43 depletion

Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian Isaacs & Vincent Plagnol
Pre-classification output of CryptEx pipeline demonstrates a variety of novel splicing events in TDP-43, FUS and hnRNP C depletion data. Every novel splicing event plotted by mean depth of reads covering the novel event against log2(fold change) between depletion and control samples. The cryptic exon classifier throws out any splicing event where the canonical intron in which the cryptic splicing event appears is represented by less than five spliced reads (purple) or where the |log2(fold...

Additional file 2: Table S2. of Development of a SNP panel dedicated to parentage assignment in French sheep populations

F. Tortereau, C. Moreno, G. Tosser-Klopp, B. Servin & J. Raoul
Results (MAF, PE1, PE2 and PI) obtained after random sampling of SNPs from the 249 SNPs selected for parentage assignment in French sheep breeds. MAF, PE1, PE2 and PI statistics were obtained after 1000 random sampling of 96, 150 and 200 SNPs. PE1 and PE2 give the probability of exclusion of one or both parents respectively, and PI gives the probability of identity. (XLSM 33 kb)

Additional file 1: of JS-K, a nitric oxide pro-drug, regulates growth and apoptosis through the ubiquitin-proteasome pathway in prostate cancer cells

Guobin Tan, Mingning Qiu, Lieqian Chen, Sai Zhang, Longzhi Ke & Jianjun Liu
IC50 results. The IC50 of LNCaP and C4-2 cell lines that treated by JS-K. (XLSX 10 kb)

Additional file 2: of JS-K, a nitric oxide pro-drug, regulates growth and apoptosis through the ubiquitin-proteasome pathway in prostate cancer cells

Guobin Tan, Mingning Qiu, Lieqian Chen, Sai Zhang, Longzhi Ke & Jianjun Liu
western blot results. The quantitation of western blot of relative protein of LNCaP and C4-2 cell lines that treated by JS-K. (XLSX 38 kb)

Additional file 1: Table S1. of Detection of ALK fusion transcripts in FFPE lung cancer samples by NanoString technology

Adriane Evangelista, Maicon Zanon, Adriana Carloni, FlĂĄvia De Paula, Mariana Morini, Maressa Ferreira-Neto, IberĂŞ Soares, Jose Miziara, Pedro De Marchi, Cristovam Scapulatempo-Neto & Rui Reis
Association of ALK fusion and the main clinico-pathological and molecular features. Summary of the major clinico-pathological characteristics of patients and RNA quality information and ALK, EGFR and KRAS status. (XLSX 14 kb)

Additional file 1: Table S1. of Development of a SNP panel dedicated to parentage assignment in French sheep populations

F. Tortereau, C. Moreno, G. Tosser-Klopp, B. Servin & J. Raoul
List of the 249 SNPs selected for Parentage assignment in French breeds. For each SNP, the genomic position is given in reference to the oar_v3.1 assembly, and the MAF is the average over the 30 French breeds included in the analysis. (XLSX 23 kb)

Additional file 2: of Exploring the heterogeneity of neural social indices for genetically distinct etiologies of autism

Caitlin Hudac, Holly Stessman, Trent DesChamps, Anna Kresse, Susan Faja, Emily Neuhaus, Sara Webb, Evan Eichler & Raphael Bernier
Genetic characterization for children with ASD is provided. Bold font highlights likely gene-disrupting mutations (LGD) associated with ASD. Abbreviations: +, present; -, absent; NC, not completed; (M), missense, (N), nonsense; (S), splice; (FS), frameshift; (IV) intronic variant. (XLSX 25 kb)

Additional file 1: of Exploring the heterogeneity of neural social indices for genetically distinct etiologies of autism

Caitlin Hudac, Holly Stessman, Trent DesChamps, Anna Kresse, Susan Faja, Emily Neuhaus, Sara Webb, Evan Eichler & Raphael Bernier
Clinical characterization for children with ASD is provided. Abbreviations: M, male; F, female; LGD, likely gene-disrupting; +, present; -, absent; NC, not completed. (XLS 47 kb)

Additional file 4 of â gnparserâ : a powerful parser for scientific names based on Parsing Expression Grammar

Dmitry Mozzherin, Alexander Myltsev & David Patterson
Extensive test suite that describes the parserâ s behavior. It is also a source of examples of parser functionality and output format. Test suite consists of a pipe delimited input (scientific name) and parsed output in JSON format. (TXT 253 kb)

Additional file 5: of Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study

Kristin Sikkink, Megan Kobiela & Emilie Snell-Rood
Summary of variable genes. Nucleotide diversity and Tajimaâ s D estimates by population for all genes containing SNPs. (XLSX 679 kb)

Additional file 4: of Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study

Kristin Sikkink, Megan Kobiela & Emilie Snell-Rood
Summary table of significant SNPs. Annotation and summary statistics for all SNPs significantly differentiated between MN and ND populations. (XLSX 93 kb)

Additional file 3: of Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study

Kristin Sikkink, Megan Kobiela & Emilie Snell-Rood
Population statistics for all SNPs. Allele frequency and population statistics for all SNPs. (XLSX 12762 kb)

Additional file 1: of Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study

Kristin Sikkink, Megan Kobiela & Emilie Snell-Rood
Phenotyping data for MN and ND individuals. Table containing the wing and development time measurements for all phenotyped individuals. (XLSX 18 kb)

Additional file 4: of Glyoxalase 1 expression is associated with an unfavorable prognosis of oropharyngeal squamous cell carcinoma

Nele Kreycy, Christiane Gotzian, Thomas Fleming, Christa Flechtenmacher, Niels Grabe, Peter Plinkert, Jochen Hess & Karim Zaoui
Table S4. Summary of the GLO1 protein level and localization as well as patient characteristics (XLSX 25 kb)

Additional file 3 of â gnparserâ : a powerful parser for scientific names based on Parsing Expression Grammar

Dmitry Mozzherin, Alexander Myltsev & David Patterson
1,000 name-strings randomly selected from GNI and used to determine Accuracy, Precision and Recall data (Table 1). (TXT 32 kb)

Additional file 3: of Glyoxalase 1 expression is associated with an unfavorable prognosis of oropharyngeal squamous cell carcinoma

Nele Kreycy, Christiane Gotzian, Thomas Fleming, Christa Flechtenmacher, Niels Grabe, Peter Plinkert, Jochen Hess & Karim Zaoui
Table S3. Summary of the GLO1 immunoreactivity score, Arg-pyrimidine protein level and patient characteristics (XLSX 21 kb)

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