cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12965379.v1
title: Additional file 4 of MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates

description: Additional file 4: Table S4. Table of ENCODE DNase-seq and histone ChIP-seq experiments used. Contains detailed listings of ENCODE datasets used in results section “MEIRLOP identifies enriched TF binding motifs in DNase I Hypersensitive Sites”, including experiment accession IDs, download URLs, and the names of labs where the data were generated.
DOI: 10.6084/m9.figshare.12965376
title: Additional file 3 of MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates

description: Additional file 3: Table S3. Table of ENCODE ChIP-seq datasets used. Contains detailed listings of ENCODE datasets used in results section “MEIRLOP achieves similar or better accuracy on TF ChIP-seq data”, including experiment accession IDs, download URLs, and the names of labs where the data were generated.
DOI: 10.6084/m9.figshare.12965397
title: Additional file 12 of Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

description: Additional file 12: Table S4. List of the SNPs associated with fifteen different phenotypic traits. Significant SNPs were identified based on three different methods (EMMA, LFMM and MLM), the Fisher combined probability test method to combine several repetitions of phenotypic data and a 10− 5 p-value threshold. For each trait, the p-values and q-values obtained with the different methods are indicated when the p-values were significant. (XLS 349 kb)
DOI: 10.6084/m9.figshare.12965397.v1
title: Additional file 12 of Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

description: Additional file 12: Table S4. List of the SNPs associated with fifteen different phenotypic traits. Significant SNPs were identified based on three different methods (EMMA, LFMM and MLM), the Fisher combined probability test method to combine several repetitions of phenotypic data and a 10− 5 p-value threshold. For each trait, the p-values and q-values obtained with the different methods are indicated when the p-values were significant. (XLS 349 kb)
DOI: 10.6084/m9.figshare.12965400
title: Additional file 13 of Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

description: Additional file 13: Table S5. List of the genomic regions associated with four different categories of phenotypic traits. Regions were defined based on 50 kb windows around the significant SNPs detected with any of the three models. Overlapping regions were combined into a single one. Only regions detected with at least two methods were retained. The chromosome (Chr), the starting (Position 1) and ending (Position 2) positions, the size of the region (Intervals) in base pairs, the number of significant SNPs included (Sign_SNPs_nb) and the lowest p-values obtained with the different methods are indicated. Sheets “RYMV” and “Tmax”concerned the regions identified for the resistance to RYMV and the maximum temperature related variables, respectively. The sheet “Flowering” concerned regions identified with the early sowing flowering time (Early) or the late sowing flowering time (Late) traits, as indicated in the columns “Trait 1” and “Trait 2”. The sheet “Panicle” concerned regions identified with rachis length (RL), primary branch average length (PBL), primary branch internode average length (PBintL), secondary branch number (SBN), secondary branch average length (SBL), and secondary branch internode average length (SBintL), as indicated in the columns “Trait 1” and “Trait 2”.
DOI: 10.6084/m9.figshare.12965400.v1
title: Additional file 13 of Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

description: Additional file 13: Table S5. List of the genomic regions associated with four different categories of phenotypic traits. Regions were defined based on 50 kb windows around the significant SNPs detected with any of the three models. Overlapping regions were combined into a single one. Only regions detected with at least two methods were retained. The chromosome (Chr), the starting (Position 1) and ending (Position 2) positions, the size of the region (Intervals) in base pairs, the number of significant SNPs included (Sign_SNPs_nb) and the lowest p-values obtained with the different methods are indicated. Sheets “RYMV” and “Tmax”concerned the regions identified for the resistance to RYMV and the maximum temperature related variables, respectively. The sheet “Flowering” concerned regions identified with the early sowing flowering time (Early) or the late sowing flowering time (Late) traits, as indicated in the columns “Trait 1” and “Trait 2”. The sheet “Panicle” concerned regions identified with rachis length (RL), primary branch average length (PBL), primary branch internode average length (PBintL), secondary branch number (SBN), secondary branch average length (SBL), and secondary branch internode average length (SBintL), as indicated in the columns “Trait 1” and “Trait 2”.
DOI: 10.6084/m9.figshare.12965406
title: Additional file 15 of Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

description: Additional file 15: Table S7. Expert list of genes previously described as involved in flowering time in Asian rice and test of enrichment of the list of genes detected by our association analysis. Fold-enrichment and G-test associated p-value are reported for our retained threshold (p-value cutoff of 10− 5 and at least two methods to define a region) and three alternative ones (p-value cutoff of 10− 4 and two methods; p-value cutoff of 10− 5; p-value cutoff of 10− 4).
DOI: 10.6084/m9.figshare.12965406.v1
title: Additional file 15 of Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

description: Additional file 15: Table S7. Expert list of genes previously described as involved in flowering time in Asian rice and test of enrichment of the list of genes detected by our association analysis. Fold-enrichment and G-test associated p-value are reported for our retained threshold (p-value cutoff of 10− 5 and at least two methods to define a region) and three alternative ones (p-value cutoff of 10− 4 and two methods; p-value cutoff of 10− 5; p-value cutoff of 10− 4).
DOI: 10.6084/m9.figshare.12965403
title: Additional file 14 of Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

description: Additional file 14: Table S6. List of genes located in each of the regions associated with four categories of phenotypic traits. Gene ID and annotations refer to MSU7 (Kawahara et al. 2013). The region names refer to the names attributed in Table S5. (XLS 105 kb)
DOI: 10.6084/m9.figshare.12965409.v1
title: Additional file 1 of Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

description: Additional file 1: Table S1. Phenotypic data used for genome-wide association analyses. Flowering time (DFT), rachis length (RL), primary branch number (PBN), primary branch average length (PBL), secondary branch average length (SBL), primary branch internode average length (PBintL), secondary branch number (SBN), secondary branch internode average length (SBintL) and spikelet number (SpN) were evaluated in field conditions in 2012 and 2014. Resistance to RYMV was evaluated in greenhouse conditions during three experiments (RYMV1, RYMV2, RYMV3) shifted of about 1–2 months. Environmental data were extracted from the worldclim database at available sampling locations. A Principal Component Analysis was then performed on i) the whole set of variables and ii) only maximal temperature related ones. The two first axes of both these PCA were then used for association analyses and are reported in this table. A Box-Cox transformation was applied to the different data set in order to approximate the normality. The “T_” prefix was added to variables names to distinguish non-transformed and transformed variables. (XLS 161 kb)
DOI: 10.6084/m9.figshare.12965409
title: Additional file 1 of Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

description: Additional file 1: Table S1. Phenotypic data used for genome-wide association analyses. Flowering time (DFT), rachis length (RL), primary branch number (PBN), primary branch average length (PBL), secondary branch average length (SBL), primary branch internode average length (PBintL), secondary branch number (SBN), secondary branch internode average length (SBintL) and spikelet number (SpN) were evaluated in field conditions in 2012 and 2014. Resistance to RYMV was evaluated in greenhouse conditions during three experiments (RYMV1, RYMV2, RYMV3) shifted of about 1–2 months. Environmental data were extracted from the worldclim database at available sampling locations. A Principal Component Analysis was then performed on i) the whole set of variables and ii) only maximal temperature related ones. The two first axes of both these PCA were then used for association analyses and are reported in this table. A Box-Cox transformation was applied to the different data set in order to approximate the normality. The “T_” prefix was added to variables names to distinguish non-transformed and transformed variables. (XLS 161 kb)
DOI: 10.6084/m9.figshare.12965412.v1
title: Additional file 2 of Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

description: Additional file 2: Table S2. Statistics of the Shapiro-Wilkinson and Anderson-Darling normality tests, applied to the different non-transformed (a) and transformed variables (b).
DOI: 10.6084/m9.figshare.12965403.v1
title: Additional file 14 of Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

description: Additional file 14: Table S6. List of genes located in each of the regions associated with four categories of phenotypic traits. Gene ID and annotations refer to MSU7 (Kawahara et al. 2013). The region names refer to the names attributed in Table S5. (XLS 105 kb)
DOI: 10.6084/m9.figshare.12965412
title: Additional file 2 of Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

description: Additional file 2: Table S2. Statistics of the Shapiro-Wilkinson and Anderson-Darling normality tests, applied to the different non-transformed (a) and transformed variables (b).
DOI: 10.6084/m9.figshare.12965418
title: Additional file 4 of Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

description: Additional file 4: Table S3. Heritability estimates of the different traits. Heritability was estimated for each phenotypic trait: flowering time, panicule morphology and resistance to RYMV virus. The analysis was done for flowering time (FT), spikelet number (SpN), primary branch number (PBN), secondary branch number (SBN), rachis length (RL), primary branch average length (PBL), secondary branch average length (SBL), primary branch internode average length (PBintL), secondary branch internode average length (SBintL) and RYMV virus content based on the mean of estimation at 17 and 20 days after infection (RYMV). We used a mixed model to estimate the inbred line variance, the bloc, the year and the residual variance. Heritability was calculated as the ratio of the line variance divided by the line variance and the residual variance ( https://plant-breeding-genomics.extension.org/estimating-heritability-and-blups-for-traits-using-tomato-phenotypic-data/ ). (ODS 10 kb)
DOI: 10.6084/m9.figshare.12965418.v1
title: Additional file 4 of Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

description: Additional file 4: Table S3. Heritability estimates of the different traits. Heritability was estimated for each phenotypic trait: flowering time, panicule morphology and resistance to RYMV virus. The analysis was done for flowering time (FT), spikelet number (SpN), primary branch number (PBN), secondary branch number (SBN), rachis length (RL), primary branch average length (PBL), secondary branch average length (SBL), primary branch internode average length (PBintL), secondary branch internode average length (SBintL) and RYMV virus content based on the mean of estimation at 17 and 20 days after infection (RYMV). We used a mixed model to estimate the inbred line variance, the bloc, the year and the residual variance. Heritability was calculated as the ratio of the line variance divided by the line variance and the residual variance ( https://plant-breeding-genomics.extension.org/estimating-heritability-and-blups-for-traits-using-tomato-phenotypic-data/ ). (ODS 10 kb)
DOI: 10.6084/m9.figshare.12965456
title: Additional file 6 of Influences on NHS Health Check behaviours: a systematic review

description: Additional file 6:. MMAT study quality.
DOI: 10.6084/m9.figshare.12965456.v1
title: Additional file 6 of Influences on NHS Health Check behaviours: a systematic review

description: Additional file 6:. MMAT study quality.
DOI: 10.6084/m9.figshare.12965487
title: Additional file 2 of Frictional properties of anorthite (feldspar): implications for the lower boundary of the seismogenic zone

description: Additional file 2. Experimental data for friction curves. Each sheet corresponds to a friction (μ = τ/σn) vs displacement (Disp) curve in Fig. 1, where FD020 is dry, 20 °C; FD200, is dry, 200 °C; FW400 is wet, 400 °C; and so on. Friction was calculated by Eq. (1). Data from the internal load cell were used at temperatures of 20, 375, and 600 °C under dry conditions, as indicated in Table 1. Noise from the power supply for the internal heaters overlapped the data signal from the internal load cell at temperatures of 375 and 600 °C.
DOI: 10.6084/m9.figshare.12965489.v1
title: Additional file 10 of Altered brain-wide auditory networks in a zebrafish model of fragile X syndrome

description: Additional file 10. Summary of segmentation for multisensory dataset. Total number of ROIs detected per fish for the multisensory dataset in WT (n = 7) and fmr1−/− (n = 5) larvae. WB, whole brain; Tel, telencephalon; Ha, habenulae; Th, thalamus; Pr, pretectum; TeO, optic tectum; TS, torus semicircularis; Teg, tegmentum; Cb, cerebellum; rHB, remaining hindbrain (without the Cb and octavolateralis nucleus (ON)).
DOI: 10.6084/m9.figshare.12965487.v1
title: Additional file 2 of Frictional properties of anorthite (feldspar): implications for the lower boundary of the seismogenic zone

description: Additional file 2. Experimental data for friction curves. Each sheet corresponds to a friction (μ = τ/σn) vs displacement (Disp) curve in Fig. 1, where FD020 is dry, 20 °C; FD200, is dry, 200 °C; FW400 is wet, 400 °C; and so on. Friction was calculated by Eq. (1). Data from the internal load cell were used at temperatures of 20, 375, and 600 °C under dry conditions, as indicated in Table 1. Noise from the power supply for the internal heaters overlapped the data signal from the internal load cell at temperatures of 375 and 600 °C.
DOI: 10.6084/m9.figshare.12965492
title: Additional file 1 of Altered brain-wide auditory networks in a zebrafish model of fragile X syndrome

description: Additional file 1. Summary of the statistical analyses used to quantify baseline activity. Brain-wide firing rates and correlation coefficient statistics in WT (n = 5), fmr1+/− (n = 10) and fmr1−/− (n = 7) larvae.
DOI: 10.6084/m9.figshare.12965492.v1
title: Additional file 1 of Altered brain-wide auditory networks in a zebrafish model of fragile X syndrome

description: Additional file 1. Summary of the statistical analyses used to quantify baseline activity. Brain-wide firing rates and correlation coefficient statistics in WT (n = 5), fmr1+/− (n = 10) and fmr1−/− (n = 7) larvae.
DOI: 10.6084/m9.figshare.12965501
title: Additional file 4 of Altered brain-wide auditory networks in a zebrafish model of fragile X syndrome

description: Additional file 4. Summary of the statistical analyses used to quantify auditory sensitivity. P values of proportion of total ROIs responsive to all audition (not amplitude specific), and P values of mean regression coefficient for brain region-specific clusters of interest above the responsive threshold in WT (n = 5) versus fmr1−/− (n = 7) larvae at various amplitudes in dB from full volume. Th, thalamus; TS, torus semicircularis; Teg, tegmentum; octavolateralis nucleus, ON.
DOI: 10.6084/m9.figshare.12965507
title: Additional file 6 of Altered brain-wide auditory networks in a zebrafish model of fragile X syndrome

description: Additional file 6. Robust linear regression slopes of log(N) versus log(E) of the auditory sensitivity graphs. We applied a robust linear regression to the log(N) versus log(E) plots in Figure 4f, 2-way ANOVA with Sidak correction was used to compare WT (n = 5) versus fmr1−/− (n = 7) larvae at various amplitudes in dB from full volume.
DOI: 10.6084/m9.figshare.12965498
title: Additional file 3 of Altered brain-wide auditory networks in a zebrafish model of fragile X syndrome

description: Additional file 3. Summary of the statistical analyses used to quantify results from the multisensory experiment. Proportion of total, mean regression coefficient, and coefficient of determination (r2) values of ROIs in WT (n = 7) and fmr1−/− (n = 5) larvae responding to visual flow, visual loom or auditory stimuli. WB, whole brain; Tel, telencephalon; Ha, habenulae; Th, thalamus; Pr, pretectum; TeO, optic tectum; TS, torus semicircularis; Teg, tegmentum; Cb, cerebellum; rHB, remaining hindbrain (without the Cb and octavolateralis nucleus (ON)).
DOI: 10.6084/m9.figshare.12965507.v1
title: Additional file 6 of Altered brain-wide auditory networks in a zebrafish model of fragile X syndrome

description: Additional file 6. Robust linear regression slopes of log(N) versus log(E) of the auditory sensitivity graphs. We applied a robust linear regression to the log(N) versus log(E) plots in Figure 4f, 2-way ANOVA with Sidak correction was used to compare WT (n = 5) versus fmr1−/− (n = 7) larvae at various amplitudes in dB from full volume.
DOI: 10.6084/m9.figshare.12965498.v1
title: Additional file 3 of Altered brain-wide auditory networks in a zebrafish model of fragile X syndrome

description: Additional file 3. Summary of the statistical analyses used to quantify results from the multisensory experiment. Proportion of total, mean regression coefficient, and coefficient of determination (r2) values of ROIs in WT (n = 7) and fmr1−/− (n = 5) larvae responding to visual flow, visual loom or auditory stimuli. WB, whole brain; Tel, telencephalon; Ha, habenulae; Th, thalamus; Pr, pretectum; TeO, optic tectum; TS, torus semicircularis; Teg, tegmentum; Cb, cerebellum; rHB, remaining hindbrain (without the Cb and octavolateralis nucleus (ON)).
DOI: 10.6084/m9.figshare.12965489
title: Additional file 10 of Altered brain-wide auditory networks in a zebrafish model of fragile X syndrome

description: Additional file 10. Summary of segmentation for multisensory dataset. Total number of ROIs detected per fish for the multisensory dataset in WT (n = 7) and fmr1−/− (n = 5) larvae. WB, whole brain; Tel, telencephalon; Ha, habenulae; Th, thalamus; Pr, pretectum; TeO, optic tectum; TS, torus semicircularis; Teg, tegmentum; Cb, cerebellum; rHB, remaining hindbrain (without the Cb and octavolateralis nucleus (ON)).
DOI: 10.6084/m9.figshare.12965516.v1
title: Additional file 9 of Altered brain-wide auditory networks in a zebrafish model of fragile X syndrome

description: Additional file 9. Summary of segmentation for baseline and auditory sensitivity dataset. Total number of ROIs detected per fish for the baseline and auditory sensitivity dataset in WT (n = 5) and fmr1−/− (n = 7) larvae. WB, whole brain; Tel, telencephalon; Ha, habenulae; Th, thalamus; Pr, pretectum; TeO, optic tectum; TS, torus semicircularis; Teg, tegmentum; Cb, cerebellum; rHB, remaining hindbrain (without the Cb and medial octavolateralis nucleus (ON)).
DOI: 10.6084/m9.figshare.12965501.v1
title: Additional file 4 of Altered brain-wide auditory networks in a zebrafish model of fragile X syndrome

description: Additional file 4. Summary of the statistical analyses used to quantify auditory sensitivity. P values of proportion of total ROIs responsive to all audition (not amplitude specific), and P values of mean regression coefficient for brain region-specific clusters of interest above the responsive threshold in WT (n = 5) versus fmr1−/− (n = 7) larvae at various amplitudes in dB from full volume. Th, thalamus; TS, torus semicircularis; Teg, tegmentum; octavolateralis nucleus, ON.
DOI: 10.6084/m9.figshare.12965516
title: Additional file 9 of Altered brain-wide auditory networks in a zebrafish model of fragile X syndrome

description: Additional file 9. Summary of segmentation for baseline and auditory sensitivity dataset. Total number of ROIs detected per fish for the baseline and auditory sensitivity dataset in WT (n = 5) and fmr1−/− (n = 7) larvae. WB, whole brain; Tel, telencephalon; Ha, habenulae; Th, thalamus; Pr, pretectum; TeO, optic tectum; TS, torus semicircularis; Teg, tegmentum; Cb, cerebellum; rHB, remaining hindbrain (without the Cb and medial octavolateralis nucleus (ON)).
DOI: 10.6084/m9.figshare.12965547
title: Additional file 3 of A non-photosynthetic green alga illuminates the reductive evolution of plastid electron transport systems

description: Additional file 3. Table S1. Plastid-targeted protein sequences detected in the transcriptome data of chlamydomonad sp. NrCl902.
DOI: 10.6084/m9.figshare.12965538.v1
title: Additional file 15 of A non-photosynthetic green alga illuminates the reductive evolution of plastid electron transport systems

description: Additional file 15. Table S6. Parameters of the Q3 product ion scan in the positive ion mode of the mass spectrometer used in the present study.
DOI: 10.6084/m9.figshare.12965547.v1
title: Additional file 3 of A non-photosynthetic green alga illuminates the reductive evolution of plastid electron transport systems

description: Additional file 3. Table S1. Plastid-targeted protein sequences detected in the transcriptome data of chlamydomonad sp. NrCl902.
DOI: 10.6084/m9.figshare.12965556
title: Additional file 6 of A non-photosynthetic green alga illuminates the reductive evolution of plastid electron transport systems

description: Additional file 6. Table S2. Mitochondrial and cytosolic protein sequences for carbon and energy metabolisms detected in the transcriptome data of chlamydomonad sp. NrCl902.
DOI: 10.6084/m9.figshare.12965556.v1
title: Additional file 6 of A non-photosynthetic green alga illuminates the reductive evolution of plastid electron transport systems

description: Additional file 6. Table S2. Mitochondrial and cytosolic protein sequences for carbon and energy metabolisms detected in the transcriptome data of chlamydomonad sp. NrCl902.
DOI: 10.6084/m9.figshare.12965565.v1
title: Additional file 9 of A non-photosynthetic green alga illuminates the reductive evolution of plastid electron transport systems

description: Additional file 9. Table S4. Detected sequences for representative plastid metabolic functions in the non-photosynthetic eudicot plant Monotropa hypopytis.
DOI: 10.6084/m9.figshare.12965535
title: Additional file 14 of A non-photosynthetic green alga illuminates the reductive evolution of plastid electron transport systems

description: Additional file 14. Table S5. Parameters of the multiple reaction monitoring (MRM) in the positive ion mode of the mass spectrometer used in the present study.
DOI: 10.6084/m9.figshare.12965535.v1
title: Additional file 14 of A non-photosynthetic green alga illuminates the reductive evolution of plastid electron transport systems

description: Additional file 14. Table S5. Parameters of the multiple reaction monitoring (MRM) in the positive ion mode of the mass spectrometer used in the present study.