cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12234041
title: Additional file 4 of RNA-Seq and secondary metabolite analyses reveal a putative defence-transcriptome in Norway spruce (Picea abies) against needle bladder rust (Chrysomyxa rhododendri) infection

description: Additional file 4: Table S2. KEGG Orthology (KO) assignment and proportion. KO assignment to the Picea abies differentially expressed genes during infection by Chrysomyxa rhododendri and proportion of assignments at each time point. At 39 dpi symptomatic needles were compared to controls. (XLS 284 kb)
DOI: 10.6084/m9.figshare.12234044.v1
title: Additional file 6 of Glucocorticoid receptors are required effectors of TGFβ1-induced p38 MAPK signaling to advanced cancer phenotypes in triple-negative breast cancer

description: Survival data pS134-GR gene signature in TCGA via SurvExpress.
DOI: 10.6084/m9.figshare.12234032
title: Additional file 4 of Glucocorticoid receptors are required effectors of TGFβ1-induced p38 MAPK signaling to advanced cancer phenotypes in triple-negative breast cancer

description: Survival data 14-3-3ζ (YWHAZ).
DOI: 10.6084/m9.figshare.12234038
title: Additional file 5 of Glucocorticoid receptors are required effectors of TGFβ1-induced p38 MAPK signaling to advanced cancer phenotypes in triple-negative breast cancer

description: Survival data pS134-GR gene signature in METABRIC.
DOI: 10.6084/m9.figshare.12234041.v1
title: Additional file 4 of RNA-Seq and secondary metabolite analyses reveal a putative defence-transcriptome in Norway spruce (Picea abies) against needle bladder rust (Chrysomyxa rhododendri) infection

description: Additional file 4: Table S2. KEGG Orthology (KO) assignment and proportion. KO assignment to the Picea abies differentially expressed genes during infection by Chrysomyxa rhododendri and proportion of assignments at each time point. At 39 dpi symptomatic needles were compared to controls. (XLS 284 kb)
DOI: 10.6084/m9.figshare.12234032.v1
title: Additional file 4 of Glucocorticoid receptors are required effectors of TGFβ1-induced p38 MAPK signaling to advanced cancer phenotypes in triple-negative breast cancer

description: Survival data 14-3-3ζ (YWHAZ).
DOI: 10.6084/m9.figshare.12234035.v1
title: Additional file 3 of RNA-Seq and secondary metabolite analyses reveal a putative defence-transcriptome in Norway spruce (Picea abies) against needle bladder rust (Chrysomyxa rhododendri) infection

description: Additional file 3: Table S1. Differentially expressed genes. Transcripts differentially expressed in infected compared to control plants in needles at 4 dpi (A), 9 dpi (B), 21 dpi (C). At 39 dpi, infected symptomatic needles were compared to control plants (D), infected non-symptomatic needles were compared to control plants (E), and infected symptomatic needles were compared to infected non-symptomatic needles (F). Over- and under-expressed genes are highlighted in red and green respectively. (XLS 1218 kb)
DOI: 10.6084/m9.figshare.12234038.v1
title: Additional file 5 of Glucocorticoid receptors are required effectors of TGFβ1-induced p38 MAPK signaling to advanced cancer phenotypes in triple-negative breast cancer

description: Survival data pS134-GR gene signature in METABRIC.
DOI: 10.6084/m9.figshare.12234020
title: Additional file 2 of Glucocorticoid receptors are required effectors of TGFβ1-induced p38 MAPK signaling to advanced cancer phenotypes in triple-negative breast cancer

description: Expression data MAP3K5.
DOI: 10.6084/m9.figshare.12234026
title: Additional file 3 of Glucocorticoid receptors are required effectors of TGFβ1-induced p38 MAPK signaling to advanced cancer phenotypes in triple-negative breast cancer

description: Correlation between GR (NR3C1) and MAP3K5.
DOI: 10.6084/m9.figshare.12234014
title: Additional file 1 of Glucocorticoid receptors are required effectors of TGFβ1-induced p38 MAPK signaling to advanced cancer phenotypes in triple-negative breast cancer

description: Expression data 14-3-3ζ (YWHAZ).
DOI: 10.6084/m9.figshare.12234017
title: Additional file 16 of RNA-Seq and secondary metabolite analyses reveal a putative defence-transcriptome in Norway spruce (Picea abies) against needle bladder rust (Chrysomyxa rhododendri) infection

description: Additional file 16: Table S9. RT-qPCR data. Mean efficiency-corrected Cq values obtained by RT-qPCR for (A) experimental samples and (B) determination of reference gene stability. (XLS 40 kb)
DOI: 10.6084/m9.figshare.12234020.v1
title: Additional file 2 of Glucocorticoid receptors are required effectors of TGFβ1-induced p38 MAPK signaling to advanced cancer phenotypes in triple-negative breast cancer

description: Expression data MAP3K5.
DOI: 10.6084/m9.figshare.12234011
title: Additional file 15 of RNA-Seq and secondary metabolite analyses reveal a putative defence-transcriptome in Norway spruce (Picea abies) against needle bladder rust (Chrysomyxa rhododendri) infection

description: Additional file 15: Figure S6. RT-qPCR assay details. Primer sequences of RT-qPCR assays.
DOI: 10.6084/m9.figshare.12234017.v1
title: Additional file 16 of RNA-Seq and secondary metabolite analyses reveal a putative defence-transcriptome in Norway spruce (Picea abies) against needle bladder rust (Chrysomyxa rhododendri) infection

description: Additional file 16: Table S9. RT-qPCR data. Mean efficiency-corrected Cq values obtained by RT-qPCR for (A) experimental samples and (B) determination of reference gene stability. (XLS 40 kb)
DOI: 10.6084/m9.figshare.12234026.v1
title: Additional file 3 of Glucocorticoid receptors are required effectors of TGFβ1-induced p38 MAPK signaling to advanced cancer phenotypes in triple-negative breast cancer

description: Correlation between GR (NR3C1) and MAP3K5.
DOI: 10.6084/m9.figshare.12234008
title: Additional file 14 of RNA-Seq and secondary metabolite analyses reveal a putative defence-transcriptome in Norway spruce (Picea abies) against needle bladder rust (Chrysomyxa rhododendri) infection

description: Additional file 14: Table S8. Picea abies pathway hierarchy model. This model was created by merging several plant reference pathway hierarchies available at KEGG and was used to standardize the KO assignment results (Additional file 6: Table S4). (XLS 25 kb)
DOI: 10.6084/m9.figshare.12234014.v1
title: Additional file 1 of Glucocorticoid receptors are required effectors of TGFβ1-induced p38 MAPK signaling to advanced cancer phenotypes in triple-negative breast cancer

description: Expression data 14-3-3ζ (YWHAZ).
DOI: 10.6084/m9.figshare.12234005
title: Additional file 13 of RNA-Seq and secondary metabolite analyses reveal a putative defence-transcriptome in Norway spruce (Picea abies) against needle bladder rust (Chrysomyxa rhododendri) infection

description: Additional file 13: Table S7. Sequence datasets of plant species applied for KEGG Orthology (KO) assignment using the KEGG Automatic Annotation Server (KAAS). KEGG Orthology (KO) assignment was applied using the Bi-directional Best Hit (BBH) method and all datasets of dicot plants (excluding Camelina sativa, Lupinus angustifolius and Cucurbita moschata), monocot plants and a basal magnoliophyta (Amborella family) were selected as reference organisms. (XLS 1108 kb)
DOI: 10.6084/m9.figshare.12234005.v1
title: Additional file 13 of RNA-Seq and secondary metabolite analyses reveal a putative defence-transcriptome in Norway spruce (Picea abies) against needle bladder rust (Chrysomyxa rhododendri) infection

description: Additional file 13: Table S7. Sequence datasets of plant species applied for KEGG Orthology (KO) assignment using the KEGG Automatic Annotation Server (KAAS). KEGG Orthology (KO) assignment was applied using the Bi-directional Best Hit (BBH) method and all datasets of dicot plants (excluding Camelina sativa, Lupinus angustifolius and Cucurbita moschata), monocot plants and a basal magnoliophyta (Amborella family) were selected as reference organisms. (XLS 1108 kb)
DOI: 10.6084/m9.figshare.12234008.v1
title: Additional file 14 of RNA-Seq and secondary metabolite analyses reveal a putative defence-transcriptome in Norway spruce (Picea abies) against needle bladder rust (Chrysomyxa rhododendri) infection

description: Additional file 14: Table S8. Picea abies pathway hierarchy model. This model was created by merging several plant reference pathway hierarchies available at KEGG and was used to standardize the KO assignment results (Additional file 6: Table S4). (XLS 25 kb)
DOI: 10.6084/m9.figshare.12234011.v1
title: Additional file 15 of RNA-Seq and secondary metabolite analyses reveal a putative defence-transcriptome in Norway spruce (Picea abies) against needle bladder rust (Chrysomyxa rhododendri) infection

description: Additional file 15: Figure S6. RT-qPCR assay details. Primer sequences of RT-qPCR assays.
DOI: 10.6084/m9.figshare.12233855
title: Additional file 2 of Molecular characterisation and morphological description of two new species of Hepatozoon Miller, 1908 (Apicomplexa: Adeleorina: Hepatozoidae) infecting leukocytes of African leopards Panthera pardus pardus (L.)

description: Additional file 2: Table S1. Estimates of divergence using partial 18S rDNA sequences from the haemogregarines species used in the current study. Distance matrix showing ranges as percentage for the genetic p-distances between the sequences. Alignment length 1924 nt.
DOI: 10.6084/m9.figshare.12233855.v1
title: Additional file 2 of Molecular characterisation and morphological description of two new species of Hepatozoon Miller, 1908 (Apicomplexa: Adeleorina: Hepatozoidae) infecting leukocytes of African leopards Panthera pardus pardus (L.)

description: Additional file 2: Table S1. Estimates of divergence using partial 18S rDNA sequences from the haemogregarines species used in the current study. Distance matrix showing ranges as percentage for the genetic p-distances between the sequences. Alignment length 1924 nt.
DOI: 10.6084/m9.figshare.12233837
title: Additional file 1 of The natural history of infantile neuroaxonal dystrophy

description: Additional file 1.
DOI: 10.6084/m9.figshare.12233825
title: Additional file 2 of A randomized controlled trial on the effects of oxymetazoline nasal spray after dacryocystorhinostomy among adult patients

description: Additional file 2. Tabulated Data Set.
DOI: 10.6084/m9.figshare.12233837.v1
title: Additional file 1 of The natural history of infantile neuroaxonal dystrophy

description: Additional file 1.
DOI: 10.6084/m9.figshare.12233825.v1
title: Additional file 2 of A randomized controlled trial on the effects of oxymetazoline nasal spray after dacryocystorhinostomy among adult patients

description: Additional file 2. Tabulated Data Set.
DOI: 10.15468/x7jbd5
title: New Polypheretima and Pithemera (Oligochaeta: Megascolecidae) species from the Mt. Malindang Range, Mindanao Island, Philippines

description: This dataset contains the digitized treatments in Plazi based on the original journal article Aspe, Nonillon M., James, Samuel W. (2015): New Polypheretima and Pithemera (Oligochaeta: Megascolecidae) species from the Mt. Malindang Range, Mindanao Island, Philippines. Journal of Natural History 49 (37): 2233-2255, DOI: 10.1080/00222933.2015.1021875
DOI: 10.6084/m9.figshare.12233747
title: Recombination filtered alignment

description: Gubbins filtered snippy alignment of 185 E. coli genome sequences aligned to K12-MG1655 reference. From the manuscript "Whole genome sequencing analysis of porcine faecal commensal Escherichia coli carrying class 1 integrons from sows and their offspring" by Zingali et al
DOI: 10.6084/m9.figshare.12233744
title: Phylogenetic Tree

description: Newick tree file described in mansucript "Whole genome sequencing analysis of porcine faecal commensal Escherichia coli carrying class 1 integrons from sows and their offspring" by Zingali et al
DOI: 10.6084/m9.figshare.12233747.v1
title: Recombination filtered alignment

description: Gubbins filtered snippy alignment of 185 E. coli genome sequences aligned to K12-MG1655 reference. From the manuscript "Whole genome sequencing analysis of porcine faecal commensal Escherichia coli carrying class 1 integrons from sows and their offspring" by Zingali et al
DOI: 10.6084/m9.figshare.12233744.v1
title: Phylogenetic Tree

description: Newick tree file described in mansucript "Whole genome sequencing analysis of porcine faecal commensal Escherichia coli carrying class 1 integrons from sows and their offspring" by Zingali et al
DOI: 10.6084/m9.figshare.12233738
title: amazon_review sample.numbers

description: After uploading the dataset, there will be a link that contains unique id. Data can be downloaded manually.
DOI: 10.6084/m9.figshare.12233729
title: Ontogenetic changes in energetic reserves, digestive enzymes, amino acid and energy content of Lithodes santolla (Anomura: Lithodidae): Baseline for culture

description: Juvenile crabs (27.75±2.16 mm carapace length, CL) and pre-adult crabs (62.10±1.61 mm CL) of <i>L. santolla</i> in intermolt stage, were collected by scuba diving at depths of 6-12 m from the subtidal zone of the Golondrina Bay (54º 50´S 68º 21´W) in the Beagle Channel, Ushuaia. Adult crabs (106.78±4.51 mm CL) were captured in Punta Oriental (54º 50´S 68º 15´W), Beagle Channel using baited commercial traps. The crabs were transported to the aquarium facilities of the Centro Austral de Investigaciones Científicas (CADIC), Ushuaia, Tierra del Fuego, and kept in individual plastic containers with a chilled seawater recirculation system at 6-8 ºC and a photoperiod cycle of 10 h light:14 h dark. Water quality was maintained using mechanical and biological filters, and a UV-sterilizer. Under this condition, the crabs were maintained for 48 h until dissection. Glycogen was determined following Lo et al 1970. Lipids was determined according to Folch et al 1957. Total soluble protein was determined following to Bradford 1976. Glucose and L-Lactate were evaluated according to Ridgway et al 2006. Proteinase activity was determined following García-Carreño 1992. Lipase activity was determined according to Versaw et al 1989. Amino acids identification and quantification were evaluated using a high-performance liquid chromatographer (HPLC). The caloric content was obtained following Lucas 1996 and Boy et al 2009.
DOI: 10.6084/m9.figshare.12233729.v1
title: Ontogenetic changes in energetic reserves, digestive enzymes, amino acid and energy content of Lithodes santolla (Anomura: Lithodidae): Baseline for culture

description: Juvenile crabs (27.75±2.16 mm carapace length, CL) and pre-adult crabs (62.10±1.61 mm CL) of <i>L. santolla</i> in intermolt stage, were collected by scuba diving at depths of 6-12 m from the subtidal zone of the Golondrina Bay (54º 50´S 68º 21´W) in the Beagle Channel, Ushuaia. Adult crabs (106.78±4.51 mm CL) were captured in Punta Oriental (54º 50´S 68º 15´W), Beagle Channel using baited commercial traps. The crabs were transported to the aquarium facilities of the Centro Austral de Investigaciones Científicas (CADIC), Ushuaia, Tierra del Fuego, and kept in individual plastic containers with a chilled seawater recirculation system at 6-8 ºC and a photoperiod cycle of 10 h light:14 h dark. Water quality was maintained using mechanical and biological filters, and a UV-sterilizer. Under this condition, the crabs were maintained for 48 h until dissection. Glycogen was determined following Lo et al 1970. Lipids was determined according to Folch et al 1957. Total soluble protein was determined following to Bradford 1976. Glucose and L-Lactate were evaluated according to Ridgway et al 2006. Proteinase activity was determined following García-Carreño 1992. Lipase activity was determined according to Versaw et al 1989. Amino acids identification and quantification were evaluated using a high-performance liquid chromatographer (HPLC). The caloric content was obtained following Lucas 1996 and Boy et al 2009.
DOI: 10.6084/m9.figshare.12233570
title: Supplemental data repository for Skelly et al (2020) Cell Stem Cell: "Mapping the effects of genetic variation on chromatin state and gene expression reveals loci that control ground state pluripotency".

description: # Genomics of Diversity Outbred mouse embryonic stem cells<br>Notes:<br> - Any lines starting with `#` in these files are comments - Example code for analyses presented in the paper is available at https://github.com/daskelly/CellStemCell_2020_diverse_mESCs<br>The files in this directory are:<br> * CCRIX_qPCR.tsv - data supporting top panel of Figure S3 * CCRIX_self_renewal.tsv - data supporting Figure 3E * Nr5a2_ChIP.txt - data supporting Figure 4H * counts_atac_norm_DO.tsv.gz - TMM-normalized counts for ATAC-Seq peaks called in Diversity Outbred samples * counts_rna_norm_DO.tsv.gz - upper quartile-normalized counts for RNA-Seq gene expression in Diversity Outbred samples * founder_nanog_flowcytometry.tsv.gz - data supporting Figure 1D * genotype_probs.Rds - genotype probabilities used for QTL mapping. Format is 3D array (dimensions are samples x founder haplotypes x pseudomarkers) * lifr_flowcytometry.tsv.gz - data supporting Figure S4C * luciferase_assay_results.txt - data supporting Figure 4C,I * quantitative_microscopy.tsv - data supporting Figure S1 * rna_seq_counts_allele_swap_ESCs.tsv - un-normalized estimated read counts derived from RNA-Seq data processed using EMASE as described in Methods * rna_seq_counts_founder_ESCs.tsv - un-normalized estimated read counts derived from RNA-Seq data processed using EMASE as described in Methods
DOI: 10.6084/m9.figshare.12233156
title: CRIC Cervix Classification

description: Classification based on Bethesda system of 400 images from microscope slides of the uterine cervix using the conventional smear (Pap smear). Data visualisation of classification available at http://database.cric.com.br/.
DOI: 10.6084/m9.figshare.12233171
title: Extended data Table 1

description: Distribution of Scopus discontinued journals by subject sub-areas. Extended data to the project GhoS(t)copus
DOI: 10.6084/m9.figshare.12233171.v2
title: Extended data Table 1

description: Distribution of Scopus discontinued journals by subject sub-areas. Extended data to the project GhoS(t)copus
DOI: 10.6084/m9.figshare.12233192.v1
title: JGI_PICRUSt_genomes.tar.bz2

description: A fasta file containing all available genomes from the JGI genome database that are used for the default PICRUSt2 reference database.
DOI: 10.6084/m9.figshare.12233171.v1
title: Extended data Table 5

description: Distribution of Scopus discontinued journals by subject sub-areas. Extended data to the project GhoS(t)copus
DOI: 10.6084/m9.figshare.12231089
title: Parkour Vault Research

description: Data from a study conducted at undergraduate level on parkour vaulting.
DOI: 10.6084/m9.figshare.12231080
title: Sequences from Cratera new species

description: DNA sequences from some new species of land planarians from the genus <i>Cratera</i>.
DOI: 10.6084/m9.figshare.12231080.v1
title: Sequences from Cratera new species

description: DNA sequences from some new species of land planarians from the genus <i>Cratera</i>.
DOI: 10.6084/m9.figshare.12231083
title: Underlying data Table 1.xlsx

description: Standardized data extraction form with data collected. Each column represents an entry of the data extraction form used by the authors. Each row contains the data of a journal included in the analysis. <br>- revised version after peer review.
DOI: 10.6084/m9.figshare.12231083.v1
title: Extended data Table 1.xlsx

description: Datasheet with data collected for the GhoS(t)Scopus Project
DOI: 10.6084/m9.figshare.12231029
title: Elsden_Wright_high_m_Alfven_waves

description: Data to make figures from paper.
DOI: 10.6084/m9.figshare.12231026
title: Beck Anxiety Inventory Questionnaire (Responses).xlsx

description: The data provided here is the results of a survey conducted among a group of Sri Lankan's. The questionnaire included the questions from the Beck Anxiety Inventory, and they were asked to mention the level of anxiety that they thought they had, and their actual score was later calculated and displayed on the sheet as well. These are all anonymous responses.
DOI: 10.6084/m9.figshare.12231029.v1
title: Elsden_Wright_high_m_Alfven_waves

description: Data to make figures from paper.
DOI: 10.6084/m9.figshare.12230963
title: Table S1 for Roberson et al.

description: Table S1 for Roberson et al.
DOI: 10.6084/m9.figshare.12230981
title: DepressionScores.xlsx

description: The data provided here is the results of a survey conducted among a group of Sri Lankan's. The questionnaire included the questions from the Beck Depression Inventory, and they were asked to mention the level of depression that they thought they had, and their actual score was later calculated and displayed on the sheet as well. These are all anonymous responses.<br><br>
DOI: 10.21942/uva.12230834
title: Supplementary file geodatabase containing Terceira GIS data

description: GIS data files with metadata used to calculate the changes in surface area over a 120 ka period in 10 ka time bins on the volcanically active island of Terceira (Azores). We took into account changes in sea level and subsidence during the analyses, and we did all analyses in ESRI ArcGIS 10.2.2 desktop software in WGS_1984_UTM_Zone_26N Transverse Mercator projection which resulted in minimal area distorations (&lt;1%) for the scale of our analysis (1-100 km<sup>2</sup>).<br> <i>Citation</i>:<br> Kenneth F. Rijsdijk, Simon Buijs, Rui Quartau, Robin Aguilée, Sietze J. Norder, Sérgio P. Ávila, Sara Maria Teixeira de Medeiros, João Carlos Carreiro Nunes, Rui Bento Elias, Carlos Melo, Paulo Stocchi, Stacy Shinneman, Erik Koene, A.C. (Harry) Seijmonsbergen, W. M. (Thijs) de Boer, Paulo A. V. Borges (2020): Recent geospatial dynamics of Terceira (Azores, Portugal) and the theoretic implications for the biogeography of active volcanic islands. Frontiers of Biogeography - Original Research Paper.<br> <i>Dataset contents</i> A file geodatabase with: Thirteen polygon shapefiles of contours reconstructed for Terceira in time bins of 10 ka for 120 ka until present. The name of volcanic origin (Cinco Picos Volcano, Guillerme Moniz Volcano, Pico Alto Volcano, Santa Barbara Volcano, Basaltic Fissural Area), the age of the event, area and shape of each polygon are included in the attribute tables. Three polygon shapefiles of contours for 141, 270 and 370 ka used for analyses. European Marine Observation and Data Network (EMODNet) bathymetry raster dataset downloaded from EMODnet Bathymetry portal (http://www.emodnet-bathymetry.eu) and clipped to study area and immediate surroundings