cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6916583
title: Additional file 3: of Three-dimensional evaluation of murine ovarian follicles using a modified CUBIC tissue clearing method

description: GFP immunohistochemistry using ovaries of CAG-EGFP mice. Female CAG-EGFP mice were fixed with the transcardial perfusion of 4% PFA. Sections were stained with Hoechst 33,342 and anti-GFP antibody to reveal the expression of EGFP protein. Note that although GFP fluorescence was undetectable in granulosa cells, the expression of immunoreactive EGFP protein was detected. Scale bars, 100Â Îźm. ( 668 kb)
DOI: 10.6084/m9.figshare.6916586.v1
title: Additional file 4: of eQTL discovery and their association with severe equine asthma in European Warmblood horses

description: Association of ATF7IP2, and GLIPR1L2 gene expression to RAO disease status. Html output of an R markdown document. The file contains one multiple logistic regression for each gene ATF7IP2, and GLIPR1L2. These models quantify the association between gene expression in ATF7IP2, or GLIPR1L2 and disease status. Four significant surrogate variables were calculated for the HDE treatment by SVA and therefore none were included in the model. An R markdown document that generated this html file is available on GitHub: https://github.com/VCMason . (HTML 866 kb)
DOI: 10.7910/dvn/jdfd2b/lcxjda
title: 0-75V-44

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6916583.v1
title: Additional file 3: of Three-dimensional evaluation of murine ovarian follicles using a modified CUBIC tissue clearing method

description: GFP immunohistochemistry using ovaries of CAG-EGFP mice. Female CAG-EGFP mice were fixed with the transcardial perfusion of 4% PFA. Sections were stained with Hoechst 33,342 and anti-GFP antibody to reveal the expression of EGFP protein. Note that although GFP fluorescence was undetectable in granulosa cells, the expression of immunoreactive EGFP protein was detected. Scale bars, 100Â Îźm. ( 668 kb)
DOI: 10.7910/dvn/jdfd2b/ddk1xs
title: 0-75V-47

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6916577
title: Additional file 3: of eQTL discovery and their association with severe equine asthma in European Warmblood horses

description: Association of DEXI and NSUN2 gene expression to RAO disease status. Html output of an R markdown document. The file contains two multiple logistic regressions and one simple logistic regression showing the association between DEXI gene expression and disease status. Multiple logistic regression with known confounders as independent variables, and the simple logistic regression only has the independent variable of interest (DEXI or NSUN2 gene expression) as the single covariate. An R markdown document that generated this html file is available on GitHub: https://github.com/VCMason . (HTML 844 kb)
DOI: 10.6084/m9.figshare.6916577.v1
title: Additional file 3: of eQTL discovery and their association with severe equine asthma in European Warmblood horses

description: Association of DEXI and NSUN2 gene expression to RAO disease status. Html output of an R markdown document. The file contains two multiple logistic regressions and one simple logistic regression showing the association between DEXI gene expression and disease status. Multiple logistic regression with known confounders as independent variables, and the simple logistic regression only has the independent variable of interest (DEXI or NSUN2 gene expression) as the single covariate. An R markdown document that generated this html file is available on GitHub: https://github.com/VCMason . (HTML 844 kb)
DOI: 10.7910/dvn/jdfd2b/p8a76n
title: 0-75V-30

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/dshntk
title: 0-75V-23

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/ikfjm1
title: 0-75V-39

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6916562
title: Additional file 2: of eQTL discovery and their association with severe equine asthma in European Warmblood horses

description: Linear mixed models jointly modeling MCK and HDE. Linear mixed models with random intercepts for each individual model the association between the top fifteen RAO associated SNPs that were also eSNPs in either MCK or HDE (chr13.32843309, chr13.32844446, chr13.33460982, chr13.33502488, chr28.3692072, chr21.52625145) and the gene expression of the genes they regulated (DEXI, NSUN2, ATF7IP2, GLIPR1L2) with reduced maximum likelihood (REML) and maximum likelihood (ML). An R markdown document that generated this html file is available on GitHub: https://github.com/VCMason . (HTML 5545 kb)
DOI: 10.7910/dvn/jdfd2b/mazyev
title: 0-75V-40

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6916562.v1
title: Additional file 2: of eQTL discovery and their association with severe equine asthma in European Warmblood horses

description: Linear mixed models jointly modeling MCK and HDE. Linear mixed models with random intercepts for each individual model the association between the top fifteen RAO associated SNPs that were also eSNPs in either MCK or HDE (chr13.32843309, chr13.32844446, chr13.33460982, chr13.33502488, chr28.3692072, chr21.52625145) and the gene expression of the genes they regulated (DEXI, NSUN2, ATF7IP2, GLIPR1L2) with reduced maximum likelihood (REML) and maximum likelihood (ML). An R markdown document that generated this html file is available on GitHub: https://github.com/VCMason . (HTML 5545 kb)
DOI: 10.7910/dvn/jdfd2b/ki2uyx
title: 0-75V-35

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/7x6yhu
title: 0-75V-45

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/z9fvoa
title: 0-75V-48

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/xemkwo
title: 0-75V-29

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/ulphov
title: 0-75V-24

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/mpvd00
title: 0-75V-9

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/cpfnju
title: 0-75V-7

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/dyot7i
title: 0-75V-14

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/z6aefb
title: 0-75V-13

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/qglich
title: 0-75V

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/a1ligb
title: 0-75V-32

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/nycq61
title: 0-75V-50

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/txpqop
title: 0-75V-11

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/uxqlpw
title: 0-75V-38

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/r2ggr3
title: 0-75V-34

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/i3q8lw
title: 0-75V-1

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/remr4f
title: 0-75V-2

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/cjov2r
title: 0-75V-46

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/va6n2x
title: 0-75V-43

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/2itcau
title: 0-75V-18

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/knhulc
title: 0-75V-3

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/ppgzkp
title: 0-75V-16

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/8egvm7
title: 0-75V-42

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/grs9bx
title: 0-75V-15

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/ige95u
title: 0-75V-41

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/wpany6
title: 0-75V-37

description: sigma=0.75volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/xeqlxm
title: 1V-15

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/dyo9mf
title: 1V-13

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6916451
title: MOESM2 of Proteomic distinction of renal oncocytomas and chromophobe renal cell carcinomas

description: Additional file 2: Table S2. Overview of the &gt; 2400 proteins were identified (false-discovery rate
DOI: 10.7910/dvn/jdfd2b/s6ozjt
title: 1V-9

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6916451.v1
title: MOESM2 of Proteomic distinction of renal oncocytomas and chromophobe renal cell carcinomas

description: Additional file 2: Table S2. Overview of the &gt; 2400 proteins were identified (false-discovery rate
DOI: 10.7910/dvn/jdfd2b/6caa9p
title: 1V-56

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/per7xl
title: 1V-43

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/szdzuw
title: 1V-2

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/fjdhkt
title: 1V-27

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6916439
title: MOESM1 of Proteomic distinction of renal oncocytomas and chromophobe renal cell carcinomas

description: Additional file 1: Table S1. Labeling scheme setup.
DOI: 10.6084/m9.figshare.6916442
title: MOESM3 of Lavender- and lavandin-distilled straws: an untapped feedstock with great potential for the production of high-added value compounds and fungal enzymes

description: Additional file 3: Data S2. Excel table containing the list of the Auxiliary Activities (AAs) detected and identified in the secretomes of P. cinnabarinus BRFM137 grown on DF, DS, LF, LS or maltose (reference) as substrates.
DOI: 10.6084/m9.figshare.6916439.v1
title: MOESM1 of Proteomic distinction of renal oncocytomas and chromophobe renal cell carcinomas

description: Additional file 1: Table S1. Labeling scheme setup.
DOI: 10.6084/m9.figshare.6916442.v1
title: MOESM3 of Lavender- and lavandin-distilled straws: an untapped feedstock with great potential for the production of high-added value compounds and fungal enzymes

description: Additional file 3: Data S2. Excel table containing the list of the Auxiliary Activities (AAs) detected and identified in the secretomes of P. cinnabarinus BRFM137 grown on DF, DS, LF, LS or maltose (reference) as substrates.
DOI: 10.7910/dvn/jdfd2b/flleka
title: 1V-54

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.12888350
title: Survey dataset - SALSA WP3 (Small farms, small food businesses and sustainable food and nutrition security)

description: Survey of 892 small-scale farm households, which was conducted in 30 regions during May to August 2017, of which 25 in 14 European countries, and 5 in African countries.<br>The characterization of the reference regions can be see here: http://www.salsa.uevora.pt/reference-regions/<br>This data set formed the basis for a set of analyzes published in a SI in the scientific journal Global Food Security. Papers already published:<br>Czekaj, M., Adamsone-Fiskovica, A., Tyran, E., Kilis, E., 2020. Small farms’ resilience strategies to face economic, social, and environmental disturbances in selected regions in Poland and Latvia, Global Food Security, 26, 100416.<br>Guarín, A., Rivera, M., Pinto-Correia, T., Guiomar, N., Šūmane, S., Moreno-Pérez, O. M., 2020. A new typology of small farms in Europe. Global Food Security, 26, 100389.<br>Rivera, M., Guarín, A., Pinto-Correia, T., Almaas, H., Mur, L.A., Burns, V., Czekaj, M., Ellis, R., Galli, F., Grivins, M., Hernández, P., Karanikolas, P., Prosperi, P., Zamora, P.S., 2020. Assessing the role of small farms in regional food systems in Europe: evidence from a comparative study. Global Food Security 26: 100417.<br>Żmija, K., Fortes, A., Tia, M.N., Šūmane, S., Ayambila, S.N., Żmija, D., Satoła, Ł., Sutherland, L.-A., 2020. Small farming and generational renewal in the context of food security challenges. Global Food Security, 26, 100412.<br><br><br>
DOI: 10.7910/dvn/jdfd2b/xugqqn
title: 1V-50

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6916427
title: MOESM2 of Lavender- and lavandin-distilled straws: an untapped feedstock with great potential for the production of high-added value compounds and fungal enzymes

description: Additional file 2: Data S1. Excel table containing the list of proteins detected and identified in the secretomes of P. cinnabarinus BRFM137 grown on DS, DF, LS, LF or maltose (reference) as substrates.
DOI: 10.7910/dvn/jdfd2b/lh9l0d
title: 1V-6

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6916427.v1
title: MOESM2 of Lavender- and lavandin-distilled straws: an untapped feedstock with great potential for the production of high-added value compounds and fungal enzymes

description: Additional file 2: Data S1. Excel table containing the list of proteins detected and identified in the secretomes of P. cinnabarinus BRFM137 grown on DS, DF, LS, LF or maltose (reference) as substrates.
DOI: 10.7910/dvn/jdfd2b/lnmtlt
title: 1V-3

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6916421
title: MOESM3 of Low and heterogeneous prevalence of glucose-6-phosphate dehydrogenase deficiency in different settings in Ethiopia using phenotyping and genotyping approaches

description: Additional file 3. Genotyping overview.
DOI: 10.6084/m9.figshare.6916421.v1
title: MOESM3 of Low and heterogeneous prevalence of glucose-6-phosphate dehydrogenase deficiency in different settings in Ethiopia using phenotyping and genotyping approaches

description: Additional file 3. Genotyping overview.
DOI: 10.7910/dvn/jdfd2b/ogxoik
title: 1V-19

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/ji9shu
title: 1V-40

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/soe0br
title: 1V-12

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/mphiex
title: 1V-11

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6916403
title: MOESM2 of Low and heterogeneous prevalence of glucose-6-phosphate dehydrogenase deficiency in different settings in Ethiopia using phenotyping and genotyping approaches

description: Additional file 2. KASP Primer sequences.
DOI: 10.7910/dvn/jdfd2b/a7zjqw
title: 1V-55

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/v2uubc
title: 1V-44

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6916403.v1
title: MOESM2 of Low and heterogeneous prevalence of glucose-6-phosphate dehydrogenase deficiency in different settings in Ethiopia using phenotyping and genotyping approaches

description: Additional file 2. KASP Primer sequences.
DOI: 10.7910/dvn/jdfd2b/bcgmm0
title: 1V-41

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/gabmpu
title: 1V-21

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/qql9jr
title: 1V-52

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/gtqnbi
title: 1V-26

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/aecs6o
title: 1V-1

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6916298
title: Sequence alignment for phylogenetic tree construction

description: This alignment was used to build a tree with our MAGs, all taxa previously identified by Burgess et al. (2012) with complete genomes available on NCBI (downloaded 2017-09-06), and all archaeal and bacterial genomes previously used in Hug et al. (2016). The genomes used in this tree and a mapping file can be found on figshare.<br>(genomes in Hug et al.’s tree of life (2016): https://doi.org/10.6084/m9.figshare.6863594.v1, https://doi.org/10.6084/m9.figshare.6863744.v2, https://doi.org/10.6084/m9.figshare.6863813.v1; genomes from Burgess et al. (2012): https://doi.org/10.6084/m9.figshare.6863798.v1).<br> <br>PhyloSift builds an alignment of the concatenated sequences for a set of core markers for each taxon. We used 37 of these single-copy marker genes (ribosomal protein S2 rpsB, S10 rpsJ, L1 rplA, L22, L4/L1e rplD, L2 rplB, S9 rpsl, L3 rplC, L14b/L23e rplN, S5, S19 rpsS, S7, L16/L10E rplP, S13 rpsM, L15, L25/L23, L6 rplF, L11 rplK, L5 rplE, S12/S23, L29, S3 rpsC, S11 rpsK, L10, S8, L18P/L5E, S15P/S13e, S17, S13 rplM, L24; and translation initiation factor IF-2, metalloendopeptidase, phenylalanyl-tRNA synthetase beta subunit, phenylalanyl-tRNA synthetase alpha subunit, tRNA pseudouridine synthase B, Porphobilinogen deaminase, and ribonuclease HII; i.e., PhyloSift markers DNGNGWU00001 - DNGNGWU00040 without DNGNGWU00004, DNGNGWU00008 and DNGNGWU00038). The amino acid alignment of these 37 concatenated genes was trimmed using trimAl v.1.2. Columns with gaps in more than 5% of the sequences were removed, as well as taxa with with less than 75% of the concatenated sequences. MAGs from ARK and ZAV that did not meet this threshold were manually kept in the alignment.
DOI: 10.7910/dvn/jdfd2b/ycaa1c
title: 1V-24

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/jdfd2b/p5fyh0
title: 1V-34

description: sigma=1volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;