cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12317861.v1
title: Additional file 8 of Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder

description: Additional file 8: Supplementary Table 6. Differentially expressed gene lists for Ethanol, Stress, and Ethanol + Stress as compared to controls via the HISAT2-featureCounts-DESeq2 pipeline, filtered by significance (p &lt; 0.01).
DOI: 10.6084/m9.figshare.12317849
title: Additional file 6 of Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder

description: Additional file 6: Supplementary Table 4. Differentially expressed gene lists for Ethanol, Stress, and Ethanol + Stress as compared to controls via the kallisto-sleuth pipeline, filtered by significance (p &lt; 0.01); GO terms and KEGG pathways overrepresented (p &lt; 0.05) by transcripts significantly differentially expressed (p &lt; 0.01) for each comparison.
DOI: 10.6084/m9.figshare.12317855
title: Additional file 7 of Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder

description: Additional file 7: Supplementary Table 5. Top 25 genes for Ethanol, Stress, and Ethanol + Stress as compared to controls via the kallisto-sleuth pipeline found using the HISAT2-featureCounts-DESeq2 pipeline.
DOI: 10.6084/m9.figshare.12317849.v1
title: Additional file 6 of Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder

description: Additional file 6: Supplementary Table 4. Differentially expressed gene lists for Ethanol, Stress, and Ethanol + Stress as compared to controls via the kallisto-sleuth pipeline, filtered by significance (p &lt; 0.01); GO terms and KEGG pathways overrepresented (p &lt; 0.05) by transcripts significantly differentially expressed (p &lt; 0.01) for each comparison.
DOI: 10.6084/m9.figshare.12317855.v1
title: Additional file 7 of Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder

description: Additional file 7: Supplementary Table 5. Top 25 genes for Ethanol, Stress, and Ethanol + Stress as compared to controls via the kallisto-sleuth pipeline found using the HISAT2-featureCounts-DESeq2 pipeline.
DOI: 10.6084/m9.figshare.12850439
title: Nucleotide_sequences

description: Gene predictions from assembly file.
DOI: 10.6084/m9.figshare.12317834
title: Additional file 3 of Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder

description: Additional file 3: Supplementary Table 2. Correlation coefficients and p-values of module-trait associations for each of the 44 modules produced by WGCNA and 11 traits.
DOI: 10.6084/m9.figshare.12317840
title: Additional file 2 of Evolutionary correlation of water-related traits between different structures of Dendrobium plants

description: Additional file 2: Table S1. The studied plant species and their water-related traits.
DOI: 10.6084/m9.figshare.12317843
title: Additional file 4 of Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder

description: Additional file 4: Supplementary Table 3. Genes implicated by transcripts in Module 19 associated with the experimental treatment group and the number of center zone entries in the open field test; GO terms and KEGG pathways overrepresented (p &lt; 0.05) in module 19.
DOI: 10.6084/m9.figshare.12850439.v1
title: Nucleotide_sequences

description: Gene predictions from assembly file.
DOI: 10.6084/m9.figshare.12317834.v1
title: Additional file 3 of Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder

description: Additional file 3: Supplementary Table 2. Correlation coefficients and p-values of module-trait associations for each of the 44 modules produced by WGCNA and 11 traits.
DOI: 10.6084/m9.figshare.12317843.v1
title: Additional file 4 of Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder

description: Additional file 4: Supplementary Table 3. Genes implicated by transcripts in Module 19 associated with the experimental treatment group and the number of center zone entries in the open field test; GO terms and KEGG pathways overrepresented (p &lt; 0.05) in module 19.
DOI: 10.6084/m9.figshare.12317828
title: Additional file 1 of Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder

description: Additional file 1: Supplementary Table 1. Read mapping statistics following RNA-Seq and pseudoalignment of reads via kallisto, alignment via HISAT2 and feature association using featureCounts.
DOI: 10.6084/m9.figshare.12317840.v1
title: Additional file 2 of Evolutionary correlation of water-related traits between different structures of Dendrobium plants

description: Additional file 2: Table S1. The studied plant species and their water-related traits.
DOI: 10.6084/m9.figshare.12317828.v1
title: Additional file 1 of Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder

description: Additional file 1: Supplementary Table 1. Read mapping statistics following RNA-Seq and pseudoalignment of reads via kallisto, alignment via HISAT2 and feature association using featureCounts.
DOI: 10.6084/m9.figshare.12860750
title: Data of in situ estimations of annual CH4 fluxes in soils of forests worldwide used from a submitted paper to Global Change Biology

description: Database containing <i>in situ</i> measures of soil CH<sub>4</sub> fluxes in forests obtained from peer-reviewed papers existing in database previously compiled and published by Castaldi et al (2006); Dutaur & Verchot (2007); Feng et al. (2020) and Ni & Groffman (2018); and from Scopus ® (Elsevier B.V.). Estimations were obtained from those studies with measurements of soil CH<sub>4</sub> fluxes using the static chamber method and gas chromatography technique, reporting soil CH<sub>4</sub> fluxes values as averages at annual temporal resolution, and that represent field conditions without additional experimental treatments (i.e. control or unmanaged plots). We collected 478 observational units from different forests around the world and from 191 peer-reviewd papers. Aditionally, we characterized each observational unit with measurements of climatic, soil and anthropogenic drivers obtained from several sources detailed in Metadata tab from archive.
DOI: 10.6084/m9.figshare.12860750.v1
title: Data of in situ estimations of annual CH4 fluxes in soils of forests worldwide used from a submitted paper to Global Change Biology

description: Database containing <i>in situ</i> measures of soil CH<sub>4</sub> fluxes in forests obtained from peer-reviewed papers existing in database previously compiled and published by Castaldi et al (2006); Dutaur & Verchot (2007); Feng et al. (2020) and Ni & Groffman (2018); and from Scopus ® (Elsevier B.V.). Estimations were obtained from those studies with measurements of soil CH<sub>4</sub> fluxes using the static chamber method and gas chromatography technique, reporting soil CH<sub>4</sub> fluxes values as averages at annual temporal resolution, and that represent field conditions without additional experimental treatments (i.e. control or unmanaged plots). We collected 478 observational units from different forests around the world and from 191 peer-reviewd papers. Aditionally, we characterized each observational unit with measurements of climatic, soil and anthropogenic drivers obtained from several sources detailed in Metadata tab from archive.
DOI: 10.6084/m9.figshare.12317717
title: TKOv3-BAGEL2.BayesFactor.txt

description: Bayes Factor of TKOv3 RPE-1 processed with BAGEL2
DOI: 10.6084/m9.figshare.12317714
title: Table_DepMap2018Q4_MAGeCK.txt

description: DepMap 2018 Q4 data processed with MAGeCK 0.5.5
DOI: 10.6084/m9.figshare.12317714.v1
title: Table_DepMap2018Q4_MAGeCK.txt

description: DepMap 2018 Q4 data processed with MAGeCK 0.5.5
DOI: 10.6084/m9.figshare.12317717.v1
title: TKOv3-BAGEL2.BayesFactor.txt

description: Bayes Factor of TKOv3 RPE-1 processed with BAGEL2
DOI: 10.6084/m9.figshare.12317696
title: Table_DepMap2018Q4_CERES.txt

description: DepMap 2018 Q4 data (CERES, dependency score)<br>
DOI: 10.6084/m9.figshare.12317708
title: Table_DepMap2018Q4_JACKS.txt

description: DepMap 2018 Q4 data processed with JACKS
DOI: 10.6084/m9.figshare.12317669
title: Table_DepMap2018Q4_BAGEL2_ONLY.txt

description: DepMap 2018 Q4 data processed with BAGEL2 ONLY<br>
DOI: 10.6084/m9.figshare.12317684
title: TKOv3-RPE1-BAGEL1.BayesFactor.txt

description: Bayes Factor of RPE-1 processed with BAGEL1
DOI: 10.6084/m9.figshare.12317690
title: Table_DepMap2018Q4_BAGEL2_CRISPRcleanR.txt

description: DepMap 2018 Q4 data processed with BAGEL2 and CRISPRcleanR<br>
DOI: 10.6084/m9.figshare.12317696.v1
title: Table_DepMap2018Q4_CERES.txt

description: DepMap 2018 Q4 data (CERES, dependency score)<br>
DOI: 10.6084/m9.figshare.12317657
title: Table_DepMap2018Q4_BAGEL2_CRISPRcleanR_MultitargetingCorrected.txt

description: DepMap 2018 Q4 data processed with BAGEL2 + CRISPRcleanR + Multitargeting effect correction<br>
DOI: 10.6084/m9.figshare.12317684.v1
title: TKOv3-RPE1-BAGEL1.BayesFactor.txt

description: Bayes Factor of RPE-1 processed with BAGEL1
DOI: 10.6084/m9.figshare.12317654
title: Table_DepMap2018Q4_BAGEL1.txt

description: DepMap 2018 Q4 data processed with BAGEL1<br>
DOI: 10.6084/m9.figshare.12317669.v1
title: Table_DepMap2018Q4_BAGEL2_ONLY.txt

description: DepMap 2018 Q4 data processed with BAGEL2 ONLY<br>
DOI: 10.6084/m9.figshare.12317690.v1
title: Table_DepMap2018Q4_BAGEL2_CRISPRcleanR.txt

description: DepMap 2018 Q4 data processed with BAGEL2 and CRISPRcleanR<br>
DOI: 10.6084/m9.figshare.12317708.v1
title: Table_DepMap2018Q4_JACKS.txt

description: DepMap 2018 Q4 data processed with JACKS
DOI: 10.6084/m9.figshare.12317645
title: proton lung template

description: image for ANTsRNet::lungExtraction
DOI: 10.6084/m9.figshare.12317648
title: TCGA_RNASeq_PanCancer.RData

description: Merged TCGA RNASeq data from UCSC Xena TCGA hub, used by https://xsliulab.github.io/tumor-immunogenicity-score/
DOI: 10.6084/m9.figshare.12317639
title: Untitled Item

description: image for ANTsRNet::lungExtraction
DOI: 10.6084/m9.figshare.12317648.v1
title: TCGA_RNASeq_PanCancer.RData

description: Merged TCGA RNASeq data from UCSC Xena TCGA hub, used by https://xsliulab.github.io/tumor-immunogenicity-score/
DOI: 10.6084/m9.figshare.12317657.v1
title: Table_DepMap2018Q4_BAGEL2_CRISPRcleanR_MultitargetingCorrected.txt

description: DepMap 2018 Q4 data processed with BAGEL2 + CRISPRcleanR + Multitargeting effect correction<br>
DOI: 10.6084/m9.figshare.12317639.v1
title: Untitled Item

description: image for ANTsRNet::lungExtraction
DOI: 10.6084/m9.figshare.12317645.v1
title: proton lung template

description: image for ANTsRNet::lungExtraction
DOI: 10.6084/m9.figshare.12841328
title: final_assembly_shotgun.fasta

description: Assembly sequence from the merged and aligned DNA fragments from Shotgun metagenome sequencing, with Illumina NextSEQ 500 platform (paired-end strategy) . The assembly was used to reconstruct the microbiome present in each one of the 14 raw cow milks from wintertime.For further details about the methodology and the bioinformatic tools used see the associated article methods (doi) and the supplementary file textS1
DOI: 10.6084/m9.figshare.12841328.v1
title: final_assembly_shotgun.fasta

description: Assembly sequence from the merged and aligned DNA fragments from Shotgun metagenome sequencing, with Illumina NextSEQ 500 platform (paired-end strategy) . The assembly was used to reconstruct the microbiome present in each one of the 14 raw cow milks from wintertime.For further details about the methodology and the bioinformatic tools used see the associated article methods (doi) and the supplementary file textS1
DOI: 10.6084/m9.figshare.12317504
title: Plose One.sav

description: This data set contains perceived effect of decentralization of health services on access to care and quality of health services
DOI: 10.6084/m9.figshare.12317504.v1
title: Plose One.sav

description: This data set contains perceived effect of decentralization of health services on access to care and quality of health services
DOI: 10.6073/pasta/4fe27a45ccd16afb28ba6789d9124e3b
title: High-Frequency Water Temperature Data at Lake Lillinonah, Connecticut, USA, 2011-2015

description: Since 2011, an instrumented buoy maintained by Friends of the Lake (FOTL, friendsofthelake.org) and Fairfield University has been deployed on Lake Lillinonah (Connecticut, USA) during the summer months to collect high-frequency water quality data. The buoy is deployed early each summer and remains in the lake until late October. From 2011-2015, the instrumented buoy was equipped with a Nexsens thermistor chain, collecting data every meter from 0.1 to 12 meters and every other meter from 12 to 18 meters. Data were collected every fifteen minutes. Included in this data package are datasets containing 15-minute data as well as daily averages. Following the summer of 2015, the buoy was equipped with an RBR thermistor chain with sensors at different depths. Available data from the RBR thermistor chain (beginning in 2018) can be found in EDI package 558. Additional high-frequency water quality data for Lake Lillinonah including dissolved oxygen, specific conductance and pigment fluorescence are available in packages EDI559 and EDI560.
DOI: 10.6084/m9.figshare.12317276
title: Acclerometer data - annotated

description: Annotated dataset of each 10 participants performing different upper extremity activities while wearing 4 GeneActiv accelerometers: dominant wrist, dominant arm, thorax, non-dominant wrist.Data was collected at 100 Hz while researchers took note of start and stop time of each activities. Raw data was then uploaded to a computer and converted into 1s epochs using GeneActiv Software. The raw data files of each accelerometer were then combined and synchronized manually for each participant and activity performed to create the final dataset.A second data set with a 10s epoch is also upload, as this epoch was used for the final publication. This was created using a python script and the initial 1s epoch file.Raw accelerometer files are too voluminous to share and useless without annotations. These can be share on special request.<br>
DOI: 10.6084/m9.figshare.12317270
title: Participant demographics

description: Demographics of the study participants."Occupation" has been blinded to decrease the risk of identification.<br>
DOI: 10.6084/m9.figshare.12317276.v1
title: Acclerometer data - annotated

description: Annotated dataset of each 10 participants performing different upper extremity activities while wearing 4 GeneActiv accelerometers: dominant wrist, dominant arm, thorax, non-dominant wrist.Data was collected at 100 Hz while researchers took note of start and stop time of each activities. Raw data was then uploaded to a computer and converted into 1s epochs using GeneActiv Software. The raw data files of each accelerometer were then combined and synchronized manually for each participant and activity performed to create the final dataset.A second data set with a 10s epoch is also upload, as this epoch was used for the final publication. This was created using a python script and the initial 1s epoch file.Raw accelerometer files are too voluminous to share and useless without annotations. These can be share on special request.<br>
DOI: 10.6084/m9.figshare.12317270.v1
title: Participant demographics

description: Demographics of the study participants."Occupation" has been blinded to decrease the risk of identification.<br>
DOI: 10.6084/m9.figshare.12317123
title: Salerno et al Progenesis exported protein list.xlsx

description: To assess the hierarchical importance of multipotent differentiation compared with trophic/immunoregulatory functions of MSCs, we have undertaken a detailed analysis of how these properties change with in vitro ageing of the cells. Using in vitro differentiation and repair models and integrating transcriptomics and proteomics data, we show that the multipotent differentiation capacity of MSCs falls with increasing passage, whereas trophic repair and immunoregulatory potency are maintained. In total four cell lines were profiled using LC-MSon a QExactive HF quadrupole-Orbitrap mass spectrometer coupled to a Dionex Ultimate 3000 RSLC nano-liquid chromatograph. Cell lines were isolated from four individuals. Secretome was collected from each cell line at passage 1, 5, 10 and 15 for a total of 16 samples.
DOI: 10.6084/m9.figshare.12317219.v2
title: PPDIST: Global observation-based precipitation probability distribution climatologies

description: The Precipitation Probability DISTribution (PPDIST) dataset represents a collection of global high-resolution (0.1°) observation-based climatologies (1979–2018) of the occurrence and peak intensity of precipitation at daily and 3-hourly time scales. For more details on the dataset, please see the following open-access paper: <br><br>Beck, H. E., Westra, S., Tan, J., Pappenberger, F., Huffman, G. J., McVicar, T. R., Gründemann, G. J., Vergopolan, N., Fowler, H. J., Lewis, E., Verbist, K., and Wood, E. F.: PPDIST: global 0.1° daily and 3-hourly precipitation probability distribution climatologies (1979–2018), <i>Scientific Data</i>, in review.<br>Please cite the above-mentioned paper when using the dataset in any publication. If the dataset forms a key component of your research, we kindly ask that you give us the opportunity to comment on your results prior to publication.
DOI: 10.6084/m9.figshare.12317219.v3
title: PPDIST: Global observation-based precipitation probability distribution climatologies

description: The Precipitation Probability DISTribution (PPDIST) dataset represents a collection of global high-resolution (0.1°) observation-based climatologies (1979–2018) of the occurrence and peak intensity of precipitation at daily and 3-hourly time scales. For more details, please see the following open-access paper: <br><br>Beck, H. E., Westra, S., Tan, J., Pappenberger, F., Huffman, G. J., McVicar, T. R., Gründemann, G. J., Vergopolan, N., Fowler, H. J., Lewis, E., Verbist, K., and Wood, E. F.: PPDIST: global 0.1° daily and 3-hourly precipitation probability distribution climatologies (1979–2018), <i>Scientific Data</i>, in review.<br>Please cite the above-mentioned paper when using the dataset in any publication. If the dataset forms a key component of your research, we kindly ask that you give us the opportunity to comment on your results prior to publication.
DOI: 10.6084/m9.figshare.12317003
title: Supplementary Material for: Understanding the Role of the Clitellum in the Regeneration Events of the Earthworm <b><i>Eudrilus eugeniae</i></b>

description: Regeneration is a complex mechanism to restore lost or damaged body parts. In earthworms, regeneration capability varies among different species, and it is important to explore the mechanism behind the regeneration process. Interestingly, regeneration in earthworms is either dependent or independent of clitellum segments. In the present study, juvenile earthworms (<i>Eudrilus eugeniae</i>) were amputated at 3 different sites, namely the head, clitellum, and tail segments (at segments 10, 15, and 30, respectively), and their regeneration ability was documented using a foldscope. The amputated segments having the intact clitellum were able to heal the wounds and form the regenerative blastema. The smaller portions of the amputated segments (segments 1–10 and 1–15) without intact clitellum were unable to heal the wound, and death occurs within 12–24 h. The larger portions of the amputated segments (segments 15 and 30 to anus) without intact clitellum were able to heal the wound but lacked the regeneration capability. In control worms, alkaline phosphatase (ALP) signals were observed at the anterior tip, clitellum, and gut epithelium tissues, whereas, upon amputation, the enriched signals from the clitellum diminished, but profound signals were observed at the amputation site and regenerative blastema. Interestingly, on days 3 and 4, blastemal tips lacked ALP signals due to initiation of the differentiation process in the regeneration blastema. In summary, using a foldscope microscope, the role of the clitellum in the regeneration mechanism was indicated by ALP activity.
DOI: 10.6084/m9.figshare.12316997
title: Supplemental Tables: Moderate-intensity exercise and high-intensity interval training affect insulin sensitivity similarly in obese adults. JCEM (2020)

description: Supplemental Tables 1 and 2
DOI: 10.6084/m9.figshare.12317003.v1
title: Supplementary Material for: Understanding the Role of the Clitellum in the Regeneration Events of the Earthworm <b><i>Eudrilus eugeniae</i></b>

description: Regeneration is a complex mechanism to restore lost or damaged body parts. In earthworms, regeneration capability varies among different species, and it is important to explore the mechanism behind the regeneration process. Interestingly, regeneration in earthworms is either dependent or independent of clitellum segments. In the present study, juvenile earthworms (<i>Eudrilus eugeniae</i>) were amputated at 3 different sites, namely the head, clitellum, and tail segments (at segments 10, 15, and 30, respectively), and their regeneration ability was documented using a foldscope. The amputated segments having the intact clitellum were able to heal the wounds and form the regenerative blastema. The smaller portions of the amputated segments (segments 1–10 and 1–15) without intact clitellum were unable to heal the wound, and death occurs within 12–24 h. The larger portions of the amputated segments (segments 15 and 30 to anus) without intact clitellum were able to heal the wound but lacked the regeneration capability. In control worms, alkaline phosphatase (ALP) signals were observed at the anterior tip, clitellum, and gut epithelium tissues, whereas, upon amputation, the enriched signals from the clitellum diminished, but profound signals were observed at the amputation site and regenerative blastema. Interestingly, on days 3 and 4, blastemal tips lacked ALP signals due to initiation of the differentiation process in the regeneration blastema. In summary, using a foldscope microscope, the role of the clitellum in the regeneration mechanism was indicated by ALP activity.
DOI: 10.6084/m9.figshare.12316907
title: multipolesDB.rar

description: database of small multipoles up to 19 vertices<br>
DOI: 10.6084/m9.figshare.12316889
title: data.xls

description: <b>Population structure, pathogenicity and fungicide sensitivity of <i>Colletotrichum</i> <i>siamense </i>from different hosts in Hainan</b>
DOI: 10.6084/m9.figshare.12316889.v1
title: data.xls

description: <b>Population structure, pathogenicity and fungicide sensitivity of <i>Colletotrichum</i> <i>siamense </i>from different hosts in Hainan</b>
DOI: 10.6084/m9.figshare.12316052
title: Additional file 1 of CSN: unsupervised approach for inferring biological networks based on the genome alone

description: Additional file 1. Additional Methods and Results.
DOI: 10.6084/m9.figshare.12316061
title: Additional file 3 of CSN: unsupervised approach for inferring biological networks based on the genome alone

description: Additional file 3. Table 13b. The new 392 annotations predicted for E. coli. (C) The new 693 annotations predicted for the metagenomic sample.