cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6350120
title: Additional file 7: of Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits

description: Appendix 2. ANOVA testing the effects of TAD, CTCF and gene on ASE variation. TAD and CTCF remained significant when gene was fitted into a categorical variable in the ANOVA model, indicating that TAD and CTCF were independent factors from gene that were predictive of ASE variation. (ZIP 78 kb)
DOI: 10.6084/m9.figshare.14738630
title: Additional file 3 of CHEK1 and circCHEK1_246aa evoke chromosomal instability and induce bone lesion formation in multiple myeloma

description: Additional file 3. Supplementary Table 1 - RNA seq analysis of differentially expressed genes in osteoclast differentiation.
DOI: 10.6084/m9.figshare.14738642
title: Additional file 5 of CHEK1 and circCHEK1_246aa evoke chromosomal instability and induce bone lesion formation in multiple myeloma

description: Additional file 5. Supplementary Table 3 - Statistics of Pathway Enrichment.
DOI: 10.6084/m9.figshare.14738633
title: Additional file 4 of CHEK1 and circCHEK1_246aa evoke chromosomal instability and induce bone lesion formation in multiple myeloma

description: Additional file 4. Supplementary Table 2 - A list of interacting proteins for CHEK1.
DOI: 10.6084/m9.figshare.14738642.v1
title: Additional file 5 of CHEK1 and circCHEK1_246aa evoke chromosomal instability and induce bone lesion formation in multiple myeloma

description: Additional file 5. Supplementary Table 3 - Statistics of Pathway Enrichment.
DOI: 10.6084/m9.figshare.14738633.v1
title: Additional file 4 of CHEK1 and circCHEK1_246aa evoke chromosomal instability and induce bone lesion formation in multiple myeloma

description: Additional file 4. Supplementary Table 2 - A list of interacting proteins for CHEK1.
DOI: 10.6084/m9.figshare.14183712
title: Additional file 2 of Using electronic patient records to assess the effect of a complex antenatal intervention in a cluster randomised controlled trial—data management experience from the DESiGN Trial team

description: Additional file 2. Data dictionary. Detailed dictionary used for naming variables, describing variables and formatting variable names and values so that they were harmonised across a dataset from 13 sources.
DOI: 10.6084/m9.figshare.6350087.v1
title: Additional file 5: of Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits

description: Table S4. Enrichment of significant aseQTLs and eQTLs within bovine biological signals. This table shows the level of enrichment of each type of significant quantitative trait loci (QTLs) at biological hallmarks. Significant aseQTLs/eQTLs are defined by the P-value from aseQTL/eQTL mapping, and four P-value thresholds were tested (from 10−5 to 10−8). “&lt; 0.0001” denotes the degree of overlap between the significant aseQTLs/eQTLs and the biological hallmark larger than all permuted cases. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.14183712.v1
title: Additional file 2 of Using electronic patient records to assess the effect of a complex antenatal intervention in a cluster randomised controlled trial—data management experience from the DESiGN Trial team

description: Additional file 2. Data dictionary. Detailed dictionary used for naming variables, describing variables and formatting variable names and values so that they were harmonised across a dataset from 13 sources.
DOI: 10.6084/m9.figshare.6350138.v1
title: Additional file 12: of Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion

description: List of genes that were up- and down-regulated in M. micrantha compared with both M. cordata and M. cordifolia. (XLSX 246Â kb)
DOI: 10.6084/m9.figshare.14738670.v1
title: Additional file 1 of Aberrant expression of HDL-bound microRNA induced by a high-fat diet in a pig model: implications in the pathogenesis of dyslipidaemia

description: Additional file 1. Table S1. The sequences of the primers.
DOI: 10.6084/m9.figshare.6874382.v1
title: Additional file 2: of Integrative omics analyses broaden treatment targets in human cancer

description: Table S1. Drug classes in DEPO (database of evidence for precision oncology). Table S2. Sensitive druggable mutations in 6570 TCGA tumors. Table S3. Highest level of evidence present per variant for both resistant and sensitive. Table S4. Drugs represented in the GDSC Cell Line Data. Table S5. Cell lines that contain a sensitive mutation in DEPO. Table S6. Mann-Whitney U test of distribution of Ln(IC50) values in cell lines with DEPO sensitive mutations against background distribution for each drug. Table S7. Linear regression statistics for probe-drug pairs. Table S8. TCGA tumors (out of 3121) that are druggable based on two or more variant types (genomic, transcriptomic, proteomic). Table S9. Ten FDA-approved drug classes. Table S10. TCGA tumors that are druggable with one of ten classes of FDA-approved cancer drugs based on two or more variant types (genomic, transcriptomic, proteomic). Table S11. Druggability and demographics. Table S12. Cancer types responsible for the levels of evidence in the cancer type non-specific setting for Fig.Â 2a. Table S13. Novel druggable mutations clustering with known druggable mutations identified using HotSpot3D, a proximity-based clustering tool. Table S14. RNA-seq data and protein RPPA data for 6366 and 3877 TCGA tumors, respectively. Table S15. Druggable fusions in TCGA samples. Table S16. Evidence to support repurposing of proteogenomic alterations across cancer types. Table S17. Co-occurring druggable mutations. Table S18. Gene expression outlier scores and drug response for all cell lines. Table S19. TCGA tumors (out of 6570) that are druggable based on atleast one variant (genomic, transcriptomic, proteomic). (.xlsx 2.1Â MB) (XLSX 2039 kb)
DOI: 10.6084/m9.figshare.6874382
title: Additional file 2: of Integrative omics analyses broaden treatment targets in human cancer

description: Table S1. Drug classes in DEPO (database of evidence for precision oncology). Table S2. Sensitive druggable mutations in 6570 TCGA tumors. Table S3. Highest level of evidence present per variant for both resistant and sensitive. Table S4. Drugs represented in the GDSC Cell Line Data. Table S5. Cell lines that contain a sensitive mutation in DEPO. Table S6. Mann-Whitney U test of distribution of Ln(IC50) values in cell lines with DEPO sensitive mutations against background distribution for each drug. Table S7. Linear regression statistics for probe-drug pairs. Table S8. TCGA tumors (out of 3121) that are druggable based on two or more variant types (genomic, transcriptomic, proteomic). Table S9. Ten FDA-approved drug classes. Table S10. TCGA tumors that are druggable with one of ten classes of FDA-approved cancer drugs based on two or more variant types (genomic, transcriptomic, proteomic). Table S11. Druggability and demographics. Table S12. Cancer types responsible for the levels of evidence in the cancer type non-specific setting for Fig.Â 2a. Table S13. Novel druggable mutations clustering with known druggable mutations identified using HotSpot3D, a proximity-based clustering tool. Table S14. RNA-seq data and protein RPPA data for 6366 and 3877 TCGA tumors, respectively. Table S15. Druggable fusions in TCGA samples. Table S16. Evidence to support repurposing of proteogenomic alterations across cancer types. Table S17. Co-occurring druggable mutations. Table S18. Gene expression outlier scores and drug response for all cell lines. Table S19. TCGA tumors (out of 6570) that are druggable based on atleast one variant (genomic, transcriptomic, proteomic). (.xlsx 2.1Â MB) (XLSX 2039 kb)
DOI: 10.6084/m9.figshare.6350144.v1
title: Additional file 5: of Dynamic transcriptome profiling towards understanding the morphogenesis and development of diverse feather in domestic duck

description: Table S1. The detailed information regarding the identity of the expression profiles of DEGs from MPvsEP, LPvsMP and LPvsEP. (XLS 1357 kb)
DOI: 10.6084/m9.figshare.6350099
title: Additional file 6: of Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits

description: Table S5. EGenes are often located within the same TAD as their furthermost and most-significant aseQTL and eQTL. This table provides the results of Chi-Square test. The Chi-Square test was to examine whether the observed frequency of eGene and its linearly-furthermost, and most-significant, aseQTL/eQTL locating in the same TAD was more often than expected. The first column specifies the putative bovine TAD set. The second column specifies the bovine cell type where the aseQTL or eQTL was measured from. A minimum P-value threshold was applied to require the most-significant aseQTL and eQTL passing the P-value threshold in the aseQTL/eQTL mapping, and four P-value thresholds were tested (from 10−5 to 10−8). The expected number of the significant eSNP and eGene within the same TAD was defined as the product among the maximum number of eSNPs in a chromosome analysed during aseQTL or eQTL mapping, the number of eGenes overlapping a TAD in a TAD set, and the P-value threshold that filter the significant aseQTL/eQTL mapping results. The observed number of linearly-furthermost, and most-significant, aseQTL/eQTL and eGene within the same TAD was calculated from the data. The Chi-Square test P-values were all much smaller than 10−8, and were denoted as “&lt;10e-08” in the table. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6350099.v1
title: Additional file 6: of Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits

description: Table S5. EGenes are often located within the same TAD as their furthermost and most-significant aseQTL and eQTL. This table provides the results of Chi-Square test. The Chi-Square test was to examine whether the observed frequency of eGene and its linearly-furthermost, and most-significant, aseQTL/eQTL locating in the same TAD was more often than expected. The first column specifies the putative bovine TAD set. The second column specifies the bovine cell type where the aseQTL or eQTL was measured from. A minimum P-value threshold was applied to require the most-significant aseQTL and eQTL passing the P-value threshold in the aseQTL/eQTL mapping, and four P-value thresholds were tested (from 10−5 to 10−8). The expected number of the significant eSNP and eGene within the same TAD was defined as the product among the maximum number of eSNPs in a chromosome analysed during aseQTL or eQTL mapping, the number of eGenes overlapping a TAD in a TAD set, and the P-value threshold that filter the significant aseQTL/eQTL mapping results. The observed number of linearly-furthermost, and most-significant, aseQTL/eQTL and eGene within the same TAD was calculated from the data. The Chi-Square test P-values were all much smaller than 10−8, and were denoted as “&lt;10e-08” in the table. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6350189
title: Additional file 8: of Dynamic transcriptome profiling towards understanding the morphogenesis and development of diverse feather in domestic duck

description: Table S3. The detailed information regarding the identity of the expression profiles of DEGs from MFvsEF, LFvsMF and LFvsEF. (XLS 1656 kb)
DOI: 10.6084/m9.figshare.6350183
title: Additional file 15: of Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion

description: Identification of GO categories with accelerated evolution between invasive and non-invasive Mikania. (a) M. micrantha-M. cordata vs. M. cordata-M. cordifolia. (b) M. micrantha-M. cordifolia vs. M. cordata-M. cordifolia. (XLSX 36Â kb)
DOI: 10.6084/m9.figshare.6874481
title: Additional file 10: of Biphasic modulation of insulin signaling enables highly efficient hematopoietic differentiation from human pluripotent stem cells

description: Table S6. RNA-seq datasets from published papers used for hPSC-derived HSPC comparison (XLSX 33 kb)
DOI: 10.6084/m9.figshare.6874481.v1
title: Additional file 10: of Biphasic modulation of insulin signaling enables highly efficient hematopoietic differentiation from human pluripotent stem cells

description: Table S6. RNA-seq datasets from published papers used for hPSC-derived HSPC comparison (XLSX 33 kb)
DOI: 10.6084/m9.figshare.6874499
title: Additional file 5: of Biphasic modulation of insulin signaling enables highly efficient hematopoietic differentiation from human pluripotent stem cells

description: Table S4. GO terms of significantly upregulated genes in day 5 and day 8 HEPs in insulin-free condition (XLSX 268 kb)
DOI: 10.6084/m9.figshare.6874499.v1
title: Additional file 5: of Biphasic modulation of insulin signaling enables highly efficient hematopoietic differentiation from human pluripotent stem cells

description: Table S4. GO terms of significantly upregulated genes in day 5 and day 8 HEPs in insulin-free condition (XLSX 268 kb)
DOI: 10.6084/m9.figshare.6350210
title: Additional file 17: of Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion

description: Positively selected genes identified in (a) M. micrantha, (b) M. cordata, and (c) M. cordifolia. (XLSX 39Â kb)
DOI: 10.6084/m9.figshare.6874490.v1
title: Additional file 2: of Biphasic modulation of insulin signaling enables highly efficient hematopoietic differentiation from human pluripotent stem cells

description: Table S7. Q-PCR primers used in this study (XLSX 11 kb)
DOI: 10.6084/m9.figshare.14738739.v1
title: Additional file 2 of The effect of methanol fixation on single-cell RNA sequencing data

description: Additional file 2: Gene list used in GO analysis.
DOI: 10.6084/m9.figshare.6350132.v1
title: Additional file 8: of Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits

description: Figure S1. Runs of genes with allele-specific expression within regulatory units. Only runs of genes within TAD and between CTCF binding motifs are shown. Our ANOVA models showed that both TAD and CTCF are significant factors (P-value ≤ 10−6 and false discovery rate &lt; 0.01) explaining the observed ASE variation, while gene is a also a significant factor in Figure S1A but not a significant factor in Figure S1B. The ASE scores (y-axis) for heterozygous loci (x-axis) are plotted as black dot points in each Manhattan plot. Since ASE score was a division of paternal to maternal allelic read counts, the heterozygous locus whose ASE score is larger than 0 favours paternal expression, and the heterozygous locus whose ASE score is less than 0 favours maternal expression. The putative bovine TAD is represented as a rectangle centring at y = 0. The CTCF binding motifs (motif score ≥ 80 and motif P-value ≤ 10−8) are represented as the start and end position of each arrowed curve, where the direction of the arrow is the direction of transcription. Genes are represented as coloured bars starting from y = 0 towards either the top (gene on forward strand) or the bottom (gene on reverse strand) of the graph. Gene names or IDs from Ensembl UMD3.1 annotation (release 75) are listed in legend. (ZIP 260 kb)
DOI: 10.6084/m9.figshare.6874502
title: Additional file 6: of Biphasic modulation of insulin signaling enables highly efficient hematopoietic differentiation from human pluripotent stem cells

description: Table S2. DEseq2 gene list of significantly differentially expressed genes in day 8 HEPs in presence or absence of insulin (XLSX 303 kb)
DOI: 10.6084/m9.figshare.6350138
title: Additional file 12: of Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion

description: List of genes that were up- and down-regulated in M. micrantha compared with both M. cordata and M. cordifolia. (XLSX 246Â kb)
DOI: 10.6084/m9.figshare.3204403
title: A novel mitochondrial DNA deletion in a patient with Pearson syndrome and neonatal diabetes mellitus provides insight into disease etiology, severity and progression

description: Pearson syndrome (PS) is a rare, mitochondrial DNA (mtDNA) deletion disorder mainly affecting hematopoietic system and exocrine pancreas in early infancy, which is characterized by multi-organ involvement, variable manifestations and poor prognosis. Since the clinical complexity and uncertain outcome of PS, the ability to early diagnose and anticipate disease progression is of great clinical importance. We described a patient with severe anemia and hyperglycinemia at birth was diagnosed with neonatal diabetes mellitus, and later with PS. Genetic testing revealed that a novel mtDNA deletion existed in various non-invasive tissues from the patient. The disease course was monitored by mtDNA deletion heteroplasmy and mtDNA/nucleus DNA genome ratio in different tissues and at different time points, showing a potential genotype–phenotype correlation. Our findings suggest that for patient suspected for PS, it may be therapeutically important to first perform detailed mtDNA analysis on non-invasive tissues at the initial diagnosis and during disease progression.
DOI: 10.6084/m9.figshare.14738718
title: Additional file 1 of FOXH1 promotes lung cancer progression by activating the Wnt/β-catenin signaling pathway

description: Additional file 1: Table S1. Antibody list.
DOI: 10.6084/m9.figshare.14738718.v1
title: Additional file 1 of FOXH1 promotes lung cancer progression by activating the Wnt/β-catenin signaling pathway

description: Additional file 1: Table S1. Antibody list.
DOI: 10.6084/m9.figshare.25163669
title: Data associated with Blume-Werry et al. 2024, "<i>In-situ</i> seasonal patterns of root auxin concentrations and meristem length in an arctic sedge", New Phytologist

description: Data associated with the abovementioned manuscript: active layer thickness over time, temperature and moisture data at different soil depth, as well as root tip meristem length and auxin concentrations.
DOI: 10.6084/m9.figshare.25163699
title: Supplementary Material for: A Possible Newly Defined and Treatable Secondary Cause of Early Morning Wake-Up Headaches in an Older Hypermobile Woman: Nutcracker Physiology with Spinal Epidural Venous Congestion

description: Introduction
Left renal vein compression (nutcracker physiology) with secondary spinal epidural venous congestion is a newly recognized cause of daily persistent headache. Presently only women with underlying symptomatic hypermobility issues appear to develop headache from this anatomic issue. The hypothesized etiology is an abnormal reset of the patient’s cerebrospinal fluid (CSF) pressure to an elevated state. Headaches that occur during sleep can have a varied differential diagnosis, one of which is elevated CSF pressure. We present the case of an older woman who began to develop severe wake-up headaches at midnight. She was found to have left renal vein compression and spinal epidural venous congestion on imaging. After treatment with lumbar vein coil embolization, which alleviated the spinal cord venous congestion, her headaches alleviated.
Case Presentation 
 A 61-year-old woman with a history of hypermobile Ehlers-Danlos syndrome, began to be awakened with severe head pain at midnight at least several times per week. The headache was a holocranial, pressure sensation, which worsened in the supine position. The headaches were mostly eliminated with acetazolamide. Because of her hypermobility issues and pressure-like headache she was investigated for underlying nutcracker physiology and spinal epidural venous congestion. This was confirmed using magnetic resonance (MR) angiography and conventional venography, and after lumbar vein coil embolization her wake-up headaches ceased. 
Conclusion
The case report suggests a possible new underlying and treatable cause for early morning, wake-up, headaches: nutcracker physiology with secondary spinal epidural venous congestion. The case expands on the clinical headache presentation of nutcracker physiology.
DOI: 10.6084/m9.figshare.6874511.v1
title: Additional file 9: of Biphasic modulation of insulin signaling enables highly efficient hematopoietic differentiation from human pluripotent stem cells

description: Table S5. GO terms of significantly upregulated and downregulated genes in day 8 HSPCs versus ECs (XLSX 291 kb)
DOI: 10.6084/m9.figshare.6350156.v1
title: Additional file 13: of Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion

description: GO categories over-represented in the list of up-regulated genes in M. micrantha. (XLSX 46Â kb)
DOI: 10.6084/m9.figshare.6350165
title: Additional file 14: of Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion

description: Top 10% GO categories displaying the highest Ka/Ks ratios between two species. (a) M. micrantha-M. cordata. (b) M. micrantha-M. cordifolia. (c) M. cordata-M. cordifolia. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.6350165.v1
title: Additional file 14: of Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion

description: Top 10% GO categories displaying the highest Ka/Ks ratios between two species. (a) M. micrantha-M. cordata. (b) M. micrantha-M. cordifolia. (c) M. cordata-M. cordifolia. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.6350189.v1
title: Additional file 8: of Dynamic transcriptome profiling towards understanding the morphogenesis and development of diverse feather in domestic duck

description: Table S3. The detailed information regarding the identity of the expression profiles of DEGs from MFvsEF, LFvsMF and LFvsEF. (XLS 1656 kb)
DOI: 10.6084/m9.figshare.6874508
title: Additional file 8: of Biphasic modulation of insulin signaling enables highly efficient hematopoietic differentiation from human pluripotent stem cells

description: Table S3. DEseq2 gene list of significantly differentially expressed genes in day 8 HSPCs and ECs (XLSX 961 kb)
DOI: 10.6084/m9.figshare.3204403.v1
title: A novel mitochondrial DNA deletion in a patient with Pearson syndrome and neonatal diabetes mellitus provides insight into disease etiology, severity and progression

description: Pearson syndrome (PS) is a rare, mitochondrial DNA (mtDNA) deletion disorder mainly affecting hematopoietic system and exocrine pancreas in early infancy, which is characterized by multi-organ involvement, variable manifestations and poor prognosis. Since the clinical complexity and uncertain outcome of PS, the ability to early diagnose and anticipate disease progression is of great clinical importance. We described a patient with severe anemia and hyperglycinemia at birth was diagnosed with neonatal diabetes mellitus, and later with PS. Genetic testing revealed that a novel mtDNA deletion existed in various non-invasive tissues from the patient. The disease course was monitored by mtDNA deletion heteroplasmy and mtDNA/nucleus DNA genome ratio in different tissues and at different time points, showing a potential genotype–phenotype correlation. Our findings suggest that for patient suspected for PS, it may be therapeutically important to first perform detailed mtDNA analysis on non-invasive tissues at the initial diagnosis and during disease progression.