MOESM1 of Effects of farmersâ social networks on knowledge acquisition: lessons from agricultural training in rural Indonesia& Aya Suzuki
Additional file 1. Dataset used for effects of social networks on knowledge acquisition.
MOESM2 of Chinaâ s conversion of cropland to forest program: a systematic review of the environmental and socioeconomic effectsLucas GutiĂŠrrez RodrĂGuez, Nicholas Hogarth, Wen Zhou, Chen Xie, Kun Zhang & Louis Putzel
Additional file 2: Full bibliographies and data extraction of included studies.
Additional file 1: Table S1. of Context dependent regulatory patterns of the androgen receptor and androgen receptor target genesJan Olsen, , Margrete Hellem, Kristo Marvyin, , Yi Qu, Lisha Li, , , Anne Øyan &
Supernatant PSA assay. Various cell lines were stimulated with different combinations of growth factors and in several co-cultures. Represented here is a selection of these samples. Concentrations: R1881 (10 nm), FGF7 (10 ng/ml), PD98059 MAPKK inhibitor (30 mM), EGF (5 ng/ml) and co-culture with 50-75 % EPT1B8 cells. + denotes added growth factor. Mesenchymal EPT1 cells with p63KD (p63 knockdown), CDH1 or ΔNp63α are described in . (XLS 46 kb)
Additional file 1 of CyTRANSFINDER: a Cytoscape 3.3 plugin for three-component (TF, gene, miRNA) signal transduction pathway constructionGianfranco Politano, Francesca Orso, Monica Raimo, Alfredo Benso, Alessandro Savino, Daniela Taverna & Stefano Di Carlo
∙ srl.txt: the file containing the SRL. ∙ dgl.txt: the file containing the DGL. ∙ Indirect-miRNA-STPP.xlsx: an excel file containing the full list of 312 Indirect miRNA STPPs identified by CyTRANSFINDER using human miR-146a as the source intergenic miRNA and miR-146a 223 target genes according to TargetScan 5.2 as DGL. Results are computed using miRNA targets confirmed in at lease one source database. SmiRNA: source intragenic miRNA; TF: Transcription Factor; DG: Destination Gene. (ZIP 201...
Additional file 1 of Distributed gene expression modelling for exploring variability in epigenetic functionDavid Budden & Edmund Crampin
A single-node implementation of our code is provided for convenient reproduction of our experimental results. (ZIP 363 kb)
Fasta file containing the 48 concatenated haplotypes (409 bp of the control region + 755 bp of the cytochrome b) obtained after sequencing 331 specimens of G. aculeatus sampled in one German and 16 Ibero-balearic localities.
Genepop file containing the multilocus (18 microsatellite markers) genotypes of 478 individuals of G. aculeatus sampled in 16 localities from the Ibero-balearic region plus one German site. Eight of these loci had to be discarded from final analyses due to null alleles (stn3, stn34, stn 82, stn132, stn135, stn174 and 7033pbbe) or to the presence of unexpected intermediate alleles given the dinucleotide repeat of the locus (stn12).
Additional file 5: of Insights into the innate immunome of actiniarians using a comparative genomic approach, Peter Prentis, Joachim Surm & Ana Pavasovic
Alignment used for CniFL genes phylogenetic analysis. (FASTA 4Â kb)
Additional file 1: Table S1. of Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and MexicoAndrea Garavito, Christophe Montagnon, Romain Guyot &
List of plants evaluated with DarTseq markers. Table S2. List of DArTseq markers and used in the analysis. Table S3. Structural SNPs contributing to the population structure in C. canephora. Table S4. Putative outlier marker loci identified by the Fst outlier method implemented in Lositan. (XLSX 457Â kb)
Additional file 1: Table S1. of Analysis of microRNA (miRNA) expression profiles reveals 11 key biomarkers associated with non-small cell lung cancerKe Wang, & Wei Wu
NSCLC miRNA targets. (XLSX 296Â kb)
Additional file 4: Supplemental dataset S2. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination, Satoshi Natsume, Hiroki Takagi, , Hiroki Yaegashi, Motoki Shimizu, Kentaro Yoshida, Aiko Uemura, Kaori Oikawa, Akira Abe, Naoya Urasaki, Hideo Matsumura, , Shinsuke Yamanaka, Ryo Matsumoto, Satoru Muranaka, , Antonio Lopez-Montes, , Ranjana Bhattacharjee, Michael Abberton, , , Mai Tsujimura, Toru Terachi … & Ryohei Terauchi
Gene orthology between four angiosperms showing presence, absence, and duplication between species. (XLSX 1250 kb)
Additional file 1: Table S1. of Identification and characterization of interferon signaling-related microRNAs in occult hepatitis B virus infection, , Jing Qiu, Jie Wang, , , , Jie Zhu, & Chen Dong
Expression characteristics of selected miRNAs. (XLSX 11Â kb)
Additional file 3: of DeepCpG: accurate prediction of single-cell DNA methylation states using deep learningChristof Angermueller, Heather Lee, Wolf Reik & Oliver Stegle
Sequence motifs. HTML files with sequence logos and summary statistics for all cell types. (ZIP 19482Â kb)
Database file.Â (SAV 17 kb)
Additional file 13: of Plant pectin acetylesterase structure and function: new insights from bioinformatic analysisFlorian Philippe, Jérôme Pelloux & Catherine Rayon
Structure sequence alignment of bacterial and fungal PAEs with a fungal RGAE. The PAE sequences from some bacteria (paeY, yxiM) and fungi (yesY, rhgT, AN2528) were retrieved from Uniprot and structure-aligned with one fungal rhamnogalacturonan acetylesterase (PDB code: 1PP4) using Expresso and rendered using ESPript3 [72, 73]. Conserved residues are masked in red (absolutely conserved) or yellow. The catalytic triad in 1PP4 is indicated by a red star. Secondary structure elements of 1PP4 are shown...
MOESM3 of Three-year mortality in 30-day survivors of critical care with acute kidney injury: data from the prospective observational FINNAKI studyHenriikka Mildh, Ville Pettilä, , Sari Karlsson, Tero Ala-Kokko, Matti Reinikainen & Suvi Vaara
Additional file 3: Dataset 1. The data the paper conclusions are based on.
Additional file 2: Table S2. of Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysisPeng He, Sheng Huang, , &
RNA editing sites of Ginkgo biloba chloroplast protein-coding genes. (XLSX 26 kb)
Additional file 4: of Computational approach to predict species-specific type III secretion system (T3SS) effectors using single and multiple genomesChristopher Hobbs, Vanessa Porter, Maxwell Stow, , Herbert Tsang & Ka Leung
Comparison of top 40 predictions of T3SS effectors in S. Typhimurium, E. coli, P. syringae, and S. dysenteriae by EffectiveT3, T3MM, BPBAac, and GenSET 1. EffectiveT3 program was from Arnold et al. 2009 ; T3MM program was from Wang et al., 2013 ; and BPBAac program was from Wang et al., 2011 ; GenSET data was from this study. (XLSX 47 kb)
Additional file 5: of Computational approach to predict species-specific type III secretion system (T3SS) effectors using single and multiple genomesChristopher Hobbs, Vanessa Porter, Maxwell Stow, , Herbert Tsang & Ka Leung
A brief protocol on the setting up GenSET for T3SS effector prediction customized for other gram-negative genomes. (XLSX 40 kb)
Genome feature table for the 64 E. coli, four Shigella spp., and the one Escherichia fergusonii genomes plus accession numbers. (XLSX 18 kb)
Additional file 5: Table S2. of Identification of global regulators of T-helper cell lineage specification, Subhash Tripathi, Antti Larjo, Henrik MannerstrĂśm, , Riikka Lund, , Bing Ren, Harri LĂ¤HdesmĂ¤Ki & Riitta Lahesmaa
Table showing Jaccard similarity coefficients between platforms (XLSX 34 kb)
Additional file 1: of Development of the health literacy on social determinants of health questionnaire in Japanese adultsMasayoshi Matsumoto & Kazuhiro Nakayama
HL-SDHQ original version (Japanese version) [see Additional file 1]. (ZIP 119 kb)
Additional file 7: of TRPA1 channels promote astrocytic Ca2+ hyperactivity and synaptic dysfunction mediated by oligomeric forms of amyloid-β peptideAnthony Bosson, Adrien Paumier, Sylvie Boisseau, Muriel Jacquier-Sarlin, Alain Buisson & Mireille Albrieux
TRPA1 channels expression is located in thick GFAP-positive processes and in adjacent thin processes lacking GFAP staining. 3D–recontsruct of astrocytic processes objectivized by GFAP staining (magenta) showing that TRPA1 channels (green) expression went over in contiguous processes excluding GFAP staining. Scale bar: 50 nm. (ZIP 1736 kb)
MOESM9 of What are the environmental impacts of property rights regimes in forests, fisheries and rangelands?Maria Ojanen, Wen Zhou, Daniel Miller, Sue Nieto, & Gillian Petrokofsky
Additional file 9. Articles included for the narrative synthesis.
MOESM7 of What are the environmental impacts of property rights regimes in forests, fisheries and rangelands?Maria Ojanen, Wen Zhou, Daniel Miller, Sue Nieto, & Gillian Petrokofsky
Additional file 7. Critical appraisal of studies.