cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8480168
title: Additional file 1: of Phylogenetic analysis and embryonic expression of panarthropod Dmrt genes

description: Table S1. Primer List. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8480168.v1
title: Additional file 1: of Phylogenetic analysis and embryonic expression of panarthropod Dmrt genes

description: Table S1. Primer List. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8480150
title: Additional file 6: of Genomic analysis of serologically untypable human enteroviruses in Taiwan

description: Contributions of all enterovirus reference strain serotype. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8480144
title: Additional file 5: of Genomic analysis of serologically untypable human enteroviruses in Taiwan

description: Sequencing coverage of each NGS sample. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.8480150.v1
title: Additional file 6: of Genomic analysis of serologically untypable human enteroviruses in Taiwan

description: Contributions of all enterovirus reference strain serotype. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8480144.v1
title: Additional file 5: of Genomic analysis of serologically untypable human enteroviruses in Taiwan

description: Sequencing coverage of each NGS sample. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.8480111
title: MOESM8 of BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity

description: Additional file 8: Table S5. Same as supplementary TableÂ 4 but for K562.
DOI: 10.6084/m9.figshare.8480108
title: MOESM7 of BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity

description: Additional file 7: Table S4. Table of DESeq2 differential binding (DB) results for all TSSs in MV4;11. TSSs are represented by their gene name followed by the Refseq ID in the form name_REFSEQ_ID. This nomenclature allows us to differentiate between TSSs belonging to different transcripts of the same gene. Column names contain the information on the protein (BRD4) and the inhibitor concentration, i.e., mb4_50_1 Kb_Up.log2FoldChange corresponds to the log2 fold change of the DB analysis on MV4;11 (m), for the protein BRD4 (b4) at 50 nM of inhibitor (50) for TSS − 1 Kb (1 Kb_UP).
DOI: 10.6084/m9.figshare.8480114
title: MOESM9 of BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity

description: Additional file 9: Table S6. List of all clusters and TSSs belonging to each of them (represented by their gene and transcript name) in MV4;11 and K562 as defined in Fig.Â 3c.
DOI: 10.6084/m9.figshare.8480114.v1
title: MOESM9 of BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity

description: Additional file 9: Table S6. List of all clusters and TSSs belonging to each of them (represented by their gene and transcript name) in MV4;11 and K562 as defined in Fig.Â 3c.
DOI: 10.6084/m9.figshare.8480108.v1
title: MOESM7 of BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity

description: Additional file 7: Table S4. Table of DESeq2 differential binding (DB) results for all TSSs in MV4;11. TSSs are represented by their gene name followed by the Refseq ID in the form name_REFSEQ_ID. This nomenclature allows us to differentiate between TSSs belonging to different transcripts of the same gene. Column names contain the information on the protein (BRD4) and the inhibitor concentration, i.e., mb4_50_1 Kb_Up.log2FoldChange corresponds to the log2 fold change of the DB analysis on MV4;11 (m), for the protein BRD4 (b4) at 50 nM of inhibitor (50) for TSS − 1 Kb (1 Kb_UP).
DOI: 10.6084/m9.figshare.8480111.v1
title: MOESM8 of BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity

description: Additional file 8: Table S5. Same as supplementary TableÂ 4 but for K562.
DOI: 10.6084/m9.figshare.8480102
title: MOESM6 of BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity

description: Additional file 6: Table S3. Number of events with differential binding at TSS − 1 Kb and + 1 Kb. In addition to information in Fig. 3b, this table shows the number of TSSs affected in each condition for the indicated interval and also, the TSSs not affected in any condition (“unaffected” TSS). Percentages of affected TSSs at − 1 Kb, + 1 Kb or both is also indicated.
DOI: 10.6084/m9.figshare.8480093
title: MOESM4 of BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity

description: Additional file 4: Table S2. Number of peaks called for each condition and cell line, peaks falling on the TSS â /+ 1Â Kb, those present in H3K27ac marked regions excluding TSS â /+ 1Â Kb and remaining peaks.
DOI: 10.6084/m9.figshare.8480102.v1
title: MOESM6 of BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity

description: Additional file 6: Table S3. Number of events with differential binding at TSS − 1 Kb and + 1 Kb. In addition to information in Fig. 3b, this table shows the number of TSSs affected in each condition for the indicated interval and also, the TSSs not affected in any condition (“unaffected” TSS). Percentages of affected TSSs at − 1 Kb, + 1 Kb or both is also indicated.
DOI: 10.6084/m9.figshare.8480093.v1
title: MOESM4 of BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity

description: Additional file 4: Table S2. Number of peaks called for each condition and cell line, peaks falling on the TSS â /+ 1Â Kb, those present in H3K27ac marked regions excluding TSS â /+ 1Â Kb and remaining peaks.
DOI: 10.6084/m9.figshare.8480075
title: MOESM1 of BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity

description: Additional file 1: Table S1. Counts of raw and processed reads for each assay (ChIP-seq or Chem-Seq), protein (BRD2/3/4), condition (DMSO, 50Â nM, 500Â nM or 5000Â nM) and cell line (MV4;11 and K562) used. Percentage of uniquely mapped reads is also shown.
DOI: 10.6084/m9.figshare.8480075.v1
title: MOESM1 of BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity

description: Additional file 1: Table S1. Counts of raw and processed reads for each assay (ChIP-seq or Chem-Seq), protein (BRD2/3/4), condition (DMSO, 50Â nM, 500Â nM or 5000Â nM) and cell line (MV4;11 and K562) used. Percentage of uniquely mapped reads is also shown.
DOI: 10.6084/m9.figshare.8480063
title: MOESM11 of BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity

description: Additional file 11: Table S7. Table of DESeq2 differential expression (DE) in MV4;11 representing for each gene (ensID and symbol) the log fold change and adjusted p value for all inhibitor concentrations using DMSO as a reference.
DOI: 10.6084/m9.figshare.8480066
title: MOESM12 of BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity

description: Additional file 12: Table S8. Same as supplementary TableÂ 7 but for K562.
DOI: 10.6084/m9.figshare.8480066.v1
title: MOESM12 of BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity

description: Additional file 12: Table S8. Same as supplementary TableÂ 7 but for K562.
DOI: 10.6084/m9.figshare.8480063.v1
title: MOESM11 of BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity

description: Additional file 11: Table S7. Table of DESeq2 differential expression (DE) in MV4;11 representing for each gene (ensID and symbol) the log fold change and adjusted p value for all inhibitor concentrations using DMSO as a reference.
DOI: 10.6084/m9.figshare.8480039
title: Additional file 3: of Precision medicine in relapsed or refractory pediatric solid tumors: a collaborative Spanish initiative

description: Reference database. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.8480030
title: Additional file 2: of The E3 ubiquitin ligase RNF40 suppresses apoptosis in colorectal cancer cells

description: Figure S2. RNF40 knockout is lethal in colorectal cancer cells in vitro. (A) Diagram showing the approach to establish a permanent RNF40 knockout SW480 cells. Two gRNAs were targeted at intron regions before exon 3 and after exon 4 leading to a frameshift and a non-functional protein product. (B) Immunofluorescence assay showing the lack of RNF40 detection (red) when expressing GFP (green) which indicates successful transfection with the Cas9 construct. Scale bar: 10 μM. (C) A scatter plot showing the GFP-positive cells in non-transfected cells and transfected cells. Single cells were picked from the P4 population which is the shows highest GFP expression. (D) PCR amplification product detection on an agarose gel with no clone showing only the expected band (312 bp) upon successful deletion of RNF40. Control: Non transfected triplicate samples (2wA-C) of cells transfected with empty vectors, 24 h A, B, C: triplicates of SW480 cells transiently transfected with Cas9 after 24 h, 120 h A,B,C: triplicates of SW480 cells transiently transfected with Cas9 after 120 h, clones starting with M are MDA-MB-231 RNF40 knockout clones shown as comparison, clone numbers for SW480 (letter of plate, well number). (ZIP 5542 kb)
DOI: 10.6084/m9.figshare.8480039.v1
title: Additional file 3: of Precision medicine in relapsed or refractory pediatric solid tumors: a collaborative Spanish initiative

description: Reference database. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.8480030.v1
title: Additional file 2: of The E3 ubiquitin ligase RNF40 suppresses apoptosis in colorectal cancer cells

description: Figure S2. RNF40 knockout is lethal in colorectal cancer cells in vitro. (A) Diagram showing the approach to establish a permanent RNF40 knockout SW480 cells. Two gRNAs were targeted at intron regions before exon 3 and after exon 4 leading to a frameshift and a non-functional protein product. (B) Immunofluorescence assay showing the lack of RNF40 detection (red) when expressing GFP (green) which indicates successful transfection with the Cas9 construct. Scale bar: 10 μM. (C) A scatter plot showing the GFP-positive cells in non-transfected cells and transfected cells. Single cells were picked from the P4 population which is the shows highest GFP expression. (D) PCR amplification product detection on an agarose gel with no clone showing only the expected band (312 bp) upon successful deletion of RNF40. Control: Non transfected triplicate samples (2wA-C) of cells transfected with empty vectors, 24 h A, B, C: triplicates of SW480 cells transiently transfected with Cas9 after 24 h, 120 h A,B,C: triplicates of SW480 cells transiently transfected with Cas9 after 120 h, clones starting with M are MDA-MB-231 RNF40 knockout clones shown as comparison, clone numbers for SW480 (letter of plate, well number). (ZIP 5542 kb)
DOI: 10.6084/m9.figshare.8480024
title: Additional file 1: of The E3 ubiquitin ligase RNF40 suppresses apoptosis in colorectal cancer cells

description: Figure S1. Reduction of RNF40 and H2Bub1 in siRNF40 CRC cell lines. (A-B). The siRNA-mediated knockdown of RNF40 was verified at the mRNA level using qRT-PCR (A) and on protein level using western blot (B) in three independent experiments 72 h after transfection. Mean ± SEM, Students t test. (C) The knockdown of RNF40 resulted in decreased H2Bub1 levels 72 h after siRNA transfection. (ZIP 7432 kb)
DOI: 10.6084/m9.figshare.8480024.v1
title: Additional file 1: of The E3 ubiquitin ligase RNF40 suppresses apoptosis in colorectal cancer cells

description: Figure S1. Reduction of RNF40 and H2Bub1 in siRNF40 CRC cell lines. (A-B). The siRNA-mediated knockdown of RNF40 was verified at the mRNA level using qRT-PCR (A) and on protein level using western blot (B) in three independent experiments 72 h after transfection. Mean ± SEM, Students t test. (C) The knockdown of RNF40 resulted in decreased H2Bub1 levels 72 h after siRNA transfection. (ZIP 7432 kb)
DOI: 10.6084/m9.figshare.8480015
title: Additional file 2: of A survey of antimicrobial use practices of Tennessee beef producers

description: Raw data set. (XLSX 100 kb)
DOI: 10.6084/m9.figshare.8480015.v1
title: Additional file 2: of A survey of antimicrobial use practices of Tennessee beef producers

description: Raw data set. (XLSX 100 kb)
DOI: 10.6084/m9.figshare.8479997
title: Additional file 4: of Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models

description: Table S4. Drugs targeting most relevant genes (relevance&gt; 0.005) in Fanconi Anemia extended pathway, obtained from DrugBank database. First column: DrugBank ID; second column: drug name; third column: drug description; fourth column: drug status; sixth column: drug Indication. (XLSX 69 kb)
DOI: 10.6084/m9.figshare.8480000
title: Additional file 5: of Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models

description: Table S5. Enrichment analysis of the most relevant genes. First column: term detected in the enrichment analysis; second column: overlap; third column: p-value; fourth column: adjusted p-value; fifth column: Z score; sixth column combined score; seventh column genes annotated to the term. (XLSX 199 kb)
DOI: 10.6084/m9.figshare.8479997.v1
title: Additional file 4: of Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models

description: Table S4. Drugs targeting most relevant genes (relevance&gt; 0.005) in Fanconi Anemia extended pathway, obtained from DrugBank database. First column: DrugBank ID; second column: drug name; third column: drug description; fourth column: drug status; sixth column: drug Indication. (XLSX 69 kb)
DOI: 10.6084/m9.figshare.8480000.v1
title: Additional file 5: of Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models

description: Table S5. Enrichment analysis of the most relevant genes. First column: term detected in the enrichment analysis; second column: overlap; third column: p-value; fourth column: adjusted p-value; fifth column: Z score; sixth column combined score; seventh column genes annotated to the term. (XLSX 199 kb)
DOI: 10.6084/m9.figshare.8479988
title: Additional file 1: of Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models

description: Table S1. All gene drug targets studied obtained from DrugBank database version 5.1.2, ranked by their relevance obtained from MORF modelling. First column: gene name; second column: gene symbol: third column: Entrez ID; fourth column: relevance; fifth column: DrugBank ID of the drugs targeting the gene. (XLS 200 kb)
DOI: 10.6084/m9.figshare.8479988.v1
title: Additional file 1: of Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models

description: Table S1. All gene drug targets studied obtained from DrugBank database version 5.1.2, ranked by their relevance obtained from MORF modelling. First column: gene name; second column: gene symbol: third column: Entrez ID; fourth column: relevance; fifth column: DrugBank ID of the drugs targeting the gene. (XLS 200 kb)
DOI: 10.6084/m9.figshare.8479901
title: Additional file 4 of SRAssembler: Selective Recursive local Assembly of homologous genomic regions

description: FASTA-format alignment of hit contigs from 20 rice cultivars. The Os07g26940.1 CDS sequence was used as the SRAssembler query against sequencing reads from 20 rice cultivars. The hit contigs were aligned with the reference genomic sequence for Os07g26940.1 using MUSCLE. (MUSCLE 154 kb)
DOI: 10.6084/m9.figshare.8479901.v1
title: Additional file 4 of SRAssembler: Selective Recursive local Assembly of homologous genomic regions

description: FASTA-format alignment of hit contigs from 20 rice cultivars. The Os07g26940.1 CDS sequence was used as the SRAssembler query against sequencing reads from 20 rice cultivars. The hit contigs were aligned with the reference genomic sequence for Os07g26940.1 using MUSCLE. (MUSCLE 154 kb)
DOI: 10.6084/m9.figshare.8479892
title: Additional file 3 of SRAssembler: Selective Recursive local Assembly of homologous genomic regions

description: Scripts and files for complete replication of results. Unpacking this tarball will create directories and scripts that, when executed, will download all necessary reads and perform all of the experiments described in this manuscript. The scripts will reproduce all of the tables and figures in this manuscript except for the workflow diagram. (TAR 340 kb)
DOI: 10.6084/m9.figshare.8479889
title: Additional file 2 of SRAssembler: Selective Recursive local Assembly of homologous genomic regions

description: Table of Arabidopsis orthologs to rice queries and their aligned contigs. The contigs from twenty SRAssembler runs using rice proteins against Arabidopsis genomic sequencing reads were aligned with blastn against the Arabidopsis reference genome. The Arabidopsis orthologs (“Atgene”), their locations(“GeneStart” and “GeneStop”), and the beginning and end of their coding sequences (“ORFstart” and “ORFstop”) were identified with Araport Thalemine. If a contig from the SRAssembler run using the homologous rice protein (“Osprobe”) overlapped with an Arabidopsis gene location, this is noted in the “Contig” column, as is the percent identity with (“Identity”) and location on (“ContigStart” and “ContigStop”) the reference genome. The length of overlap between the contig and each gene locus (“ContigGeneOverlap”) and coding region (“ContigORFOverlap”) are noted, as are the fraction of the total gene and coding region lengths (“GeneCoverage” and “ORFCoverage”). (TSV 30 kb)
DOI: 10.6084/m9.figshare.8479892.v1
title: Additional file 3 of SRAssembler: Selective Recursive local Assembly of homologous genomic regions

description: Scripts and files for complete replication of results. Unpacking this tarball will create directories and scripts that, when executed, will download all necessary reads and perform all of the experiments described in this manuscript. The scripts will reproduce all of the tables and figures in this manuscript except for the workflow diagram. (TAR 340 kb)
DOI: 10.6084/m9.figshare.8479889.v1
title: Additional file 2 of SRAssembler: Selective Recursive local Assembly of homologous genomic regions

description: Table of Arabidopsis orthologs to rice queries and their aligned contigs. The contigs from twenty SRAssembler runs using rice proteins against Arabidopsis genomic sequencing reads were aligned with blastn against the Arabidopsis reference genome. The Arabidopsis orthologs (“Atgene”), their locations(“GeneStart” and “GeneStop”), and the beginning and end of their coding sequences (“ORFstart” and “ORFstop”) were identified with Araport Thalemine. If a contig from the SRAssembler run using the homologous rice protein (“Osprobe”) overlapped with an Arabidopsis gene location, this is noted in the “Contig” column, as is the percent identity with (“Identity”) and location on (“ContigStart” and “ContigStop”) the reference genome. The length of overlap between the contig and each gene locus (“ContigGeneOverlap”) and coding region (“ContigORFOverlap”) are noted, as are the fraction of the total gene and coding region lengths (“GeneCoverage” and “ORFCoverage”). (TSV 30 kb)
DOI: 10.6084/m9.figshare.8479529
title: Linkage statistics

description: Linkage statistics for each pair of SNPs for each population meadow-wide<br>
DOI: 10.6084/m9.figshare.8479508
title: SNPs

description: All SNPs called meadow-wide for each population.<br>
DOI: 10.6084/m9.figshare.8479502
title: Representative Genomes

description: Decontaminated, final representative genomes used for each population.<br>
DOI: 10.6084/m9.figshare.8479508.v1
title: SNPs

description: All SNPs called meadow-wide for each population.<br>
DOI: 10.6084/m9.figshare.8479358
title: FST metrics

description: per gene FST values for each gene for each population across all possible comparisons.<br>
DOI: 10.6084/m9.figshare.8479415
title: Replicate genomes

description: All 467 genomes across all 19 populations (includes all replicate genomes and the representative genome for each population).<br>
DOI: 10.6084/m9.figshare.8479352
title: Data record of the survey

description: Response of the questionnaire
DOI: 10.6084/m9.figshare.8479349
title: Nucleotide diversity

description: Per gene nucleotide diversity across the meadow for each population.<br>
DOI: 10.6084/m9.figshare.8479352.v2
title: Data record of the survey

description: Response of the questionnaire
DOI: 10.6084/m9.figshare.8479352.v1
title: Data record of the survey

description: Response of the questionnaire
DOI: 10.6084/m9.figshare.8479274
title: Dataset for: Individualized Quantification of the Benefit from Reperfusion Therapy using Stroke Predictive Models

description: Purpose: Recent imaging developments have shown the potential of voxel-based models in assessing infarct growth after stroke. Many models have been proposed but their relevance in predicting the benefit of a reperfusion therapy remains unclear. We searched for a predictive model whose volumetric predictions would identify stroke patients who are to benefit from tissue Plasminogen Activator (t-PA)-induced reperfusion. Material and Methods: Forty-five cases were used to study retrospectively stroke progression from admission to end of follow-up. Predictive approaches based on various statistical models, predictive variables, and spatial filtering methods were compared. The optimal approach was chosen according to the area under the precision-recall curve (AUPRC). The final lesion volume was then predicted assuming that the patient would or would not reperfuse. Patients with an acute lesion of ≤50 mL and a predicted reduction in presence of reperfusion &gt;6 mL, and &gt;25% of the acute lesion were classified as responders. Results: The optimal model was a logistic regression using the voxel distance to the acute lesion, the volume of the acute lesion, and Gaussian-filtered MRI contrast parameters as predictive variables. The predictions gave a median AUPRC of 0.655, a median AUC of 0.976, and a median volumetric error of 8.29mL. Nineteen patients matched the responder profile. A non-significant trend of improved reduction in NIHSS score (-42.8%, p=0.09) and in lesion volume (-78.1%, p=0.21) following reperfusion was observed for responder patients. Conclusion: Despite limited volumetric accuracy, predictive stroke models can be used to quantify the benefit of reperfusion therapies.
DOI: 10.6084/m9.figshare.8479280
title: UntitleMoral disengagement: Mediator between moral perfectionism and Machiavellianism among undergraduates?d Item

description: <b>Moral disengagement: Mediator between moral perfectionism and Machiavellianism among undergraduates?</b>
DOI: 10.6084/m9.figshare.8479301
title: vaginal microbiome 16S rDNA sequencing data

description: These are original vaginal microbiome sequencing data for the paper " Characteristics of the vaginal microbiome in cross-border female sex workers in China: a cas-control study"<br>
DOI: 10.6084/m9.figshare.8479280.v1
title: UntitleMoral disengagement: Mediator between moral perfectionism and Machiavellianism among undergraduates?d Item

description: <b>Moral disengagement: Mediator between moral perfectionism and Machiavellianism among undergraduates?</b>
DOI: 10.6084/m9.figshare.8479301.v1
title: vaginal microbiome 16S rDNA sequencing data

description: These are original vaginal microbiome sequencing data for the paper " Characteristics of the vaginal microbiome in cross-border female sex workers in China: a cas-control study"<br>