cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13533139.v1
title: Additional file 9 of nanotatoR: a tool for enhanced annotation of genomic structural variants

description: Additional file 9: Supplementary Table S8. Genes overlapping deletion variants for NA12878. Chromosome and SV breakpoint start and end are shown in: - NA12878 (Mak et.al. (2016) hg38 annotation): Overlapping genes coordinates identified in the original paper by Mak et al. 2016, with hg38 reference genome annotation. - NA12878 (Mak et.al. (2016) hg19 liftOver): Overlapping genes coordinates identified in the original paper by Mak et al. 2016, lifted over to hg19. - NA12878 (nanotatoR SVmerge annotation): Overlapping genes coordinates for NA12878 labelled by BSPQI and BSSSI enzyme (SVmerge), as annotated by nanotatoR. - NA12878 (nanotatoR DLE annotation): Overlapping genes coordinates for NA12878 labelled by DLE1 enzyme (SVmerge), as annotated by nanotatoR.
DOI: 10.6084/m9.figshare.13533121.v1
title: Additional file 3 of nanotatoR: a tool for enhanced annotation of genomic structural variants

description: Additional file 3: Supplementary Table S2. Primary gene list generated for NA24385 (GM24385) dataset filtration using the term Osteoporosis. A total of 307 genes were extracted (the UGT2B17 gene is highlighted). Columns show: Genes: Primary gene symbols. Terms: Query term associated with each gene. Each cell shows the gene symbol and, between parentheses, the query term and the database (Gene, OMIM, GTR or ClinVar) from which each gene was extracted. Clinical Significance: Only genes for which likely pathogenic or pathogenic variants were found in ClinVar are displayed in this column. The parentheses match the database order in column 2, displayed as (−, −, Pathogenic/Likely Pathogenic) to indicate the information is from ClinVar and not Gene or OMIM.
DOI: 10.6084/m9.figshare.13533139
title: Additional file 9 of nanotatoR: a tool for enhanced annotation of genomic structural variants

description: Additional file 9: Supplementary Table S8. Genes overlapping deletion variants for NA12878. Chromosome and SV breakpoint start and end are shown in: - NA12878 (Mak et.al. (2016) hg38 annotation): Overlapping genes coordinates identified in the original paper by Mak et al. 2016, with hg38 reference genome annotation. - NA12878 (Mak et.al. (2016) hg19 liftOver): Overlapping genes coordinates identified in the original paper by Mak et al. 2016, lifted over to hg19. - NA12878 (nanotatoR SVmerge annotation): Overlapping genes coordinates for NA12878 labelled by BSPQI and BSSSI enzyme (SVmerge), as annotated by nanotatoR. - NA12878 (nanotatoR DLE annotation): Overlapping genes coordinates for NA12878 labelled by DLE1 enzyme (SVmerge), as annotated by nanotatoR.
DOI: 10.6084/m9.figshare.13533124
title: Additional file 4 of nanotatoR: a tool for enhanced annotation of genomic structural variants

description: Additional file 4: Supplementary Table S3. Calculation of internal frequency for the deletion variant overlapping UGT2B17 in sample NA24385. Content of the tabs and column names is detailed in the first tab (“LegendS3”) of the Excel workbook. The columns used to calculate the filtered and unfiltered frequencies are highlighted in the del_totalData tab.
DOI: 10.6084/m9.figshare.13533124.v1
title: Additional file 4 of nanotatoR: a tool for enhanced annotation of genomic structural variants

description: Additional file 4: Supplementary Table S3. Calculation of internal frequency for the deletion variant overlapping UGT2B17 in sample NA24385. Content of the tabs and column names is detailed in the first tab (“LegendS3”) of the Excel workbook. The columns used to calculate the filtered and unfiltered frequencies are highlighted in the del_totalData tab.
DOI: 10.6084/m9.figshare.13533118
title: Additional file 2 of nanotatoR: a tool for enhanced annotation of genomic structural variants

description: Additional file 2: Supplementary Table S1. NA24385 nanotatoR-annotated structural variant results. Content of the various tabs is detailed in the first tab (“LegendS1”) of the Excel workbook. SVs reported in the indel, inv., and trans tabs have undergone the default nanotatoR filtration (found in self molecules, passed chimeric score threshold). Columns in each sheet of the workbook are either a direct output of SVcaller or appended by nanotatoR, as indicated in column 3 of the table. Details about SVcaller columns are available at https://bionanogenomics.com/wp-content/uploads/2017/03/30041-SMAP-File-Format-Specification-Sheet.pdf .
DOI: 10.6084/m9.figshare.13533130
title: Additional file 6 of nanotatoR: a tool for enhanced annotation of genomic structural variants

description: Additional file 6: Supplementary Table S5. Typical run times in minutes for the various tasks for the control sample datasets. nanotatoR functions are indicated in italics in Column 1. Processing times for the Ashkenazi trio DLE labeling dataset (Example I) are shown in Column 1 (no RNA-Seq data was available for this sample). Processing times for the singleton sample (Example II) DLE labeling and dual enzyme labeling (SVmerge) are shown in columns 2 and 3 respectively.
DOI: 10.6084/m9.figshare.13533127.v1
title: Additional file 5 of nanotatoR: a tool for enhanced annotation of genomic structural variants

description: Additional file 5: Supplementary Table S4. Calculation of BNDB database frequency for the deletion variant overlapping UGT2B17 in sample NA24385. Content of the tabs and column names is detailed in the first tab (“LegendS4”) of the Excel workbook. The columns used to calculate the filtered and unfiltered frequencies are highlighted in the GM24385_data_all tab.
DOI: 10.6084/m9.figshare.13533130.v1
title: Additional file 6 of nanotatoR: a tool for enhanced annotation of genomic structural variants

description: Additional file 6: Supplementary Table S5. Typical run times in minutes for the various tasks for the control sample datasets. nanotatoR functions are indicated in italics in Column 1. Processing times for the Ashkenazi trio DLE labeling dataset (Example I) are shown in Column 1 (no RNA-Seq data was available for this sample). Processing times for the singleton sample (Example II) DLE labeling and dual enzyme labeling (SVmerge) are shown in columns 2 and 3 respectively.
DOI: 10.6084/m9.figshare.13533121
title: Additional file 3 of nanotatoR: a tool for enhanced annotation of genomic structural variants

description: Additional file 3: Supplementary Table S2. Primary gene list generated for NA24385 (GM24385) dataset filtration using the term Osteoporosis. A total of 307 genes were extracted (the UGT2B17 gene is highlighted). Columns show: Genes: Primary gene symbols. Terms: Query term associated with each gene. Each cell shows the gene symbol and, between parentheses, the query term and the database (Gene, OMIM, GTR or ClinVar) from which each gene was extracted. Clinical Significance: Only genes for which likely pathogenic or pathogenic variants were found in ClinVar are displayed in this column. The parentheses match the database order in column 2, displayed as (−, −, Pathogenic/Likely Pathogenic) to indicate the information is from ClinVar and not Gene or OMIM.
DOI: 10.6084/m9.figshare.13533136.v1
title: Additional file 8 of nanotatoR: a tool for enhanced annotation of genomic structural variants

description: Additional file 8: Supplementary Table S7. nanotatoR annotation of structural variants in the dual-labeled sample NA12878 dataset (SVmerge output). Content of the various tabs is detailed in the first tab (“LegendS7”) of the Excel book. SVs reported in the indel, inv., and trans tabs have undergone the default nanotatoR filtration (found in self molecules, passed chimeric score threshold). Columns in each sheet of the workbook are either a direct output of SVcaller or appended by nanotatoR, as indicated in column 3 of the table. In the all_PG_OV tab, the cells containing the query genes are highlighted in purple. Details about SVcaller columns are available at https://bionanogenomics.com/wp-content/uploads/2017/03/30041-SMAP-File-Format-Specification-Sheet.pdf
DOI: 10.6084/m9.figshare.13533112
title: Additional file 10 of nanotatoR: a tool for enhanced annotation of genomic structural variants

description: Additional file 10: Supplementary Table S9. Variant annotation for DMD samples. Singleton samples CDMD_1003 and CDMD_1159 were analyzed with single DLE labeling and are shown in the SingleLabel_Solo tab. Singleton samples CDMD_1155, CDMD_1156, and CDMD_1187 were analyzed with dual enzyme labeling and are shown in the DualLabel_Solo tab. Mother proband dyads CDMD_1131, CDMD_1157, and CDMD_1163 were analyzed with dual enzyme labeling and are shown in the DualLabelDuo tab. The columns used for Table 1 are highlighted. Columns in each sheet of the workbook are either a direct output of SVcaller or appended by nanotatoR, as indicated in column 3 of the table in the first tab (“Legend S9”). Details about SVcaller columns are available at https://bionanogenomics.com/wp-content/uploads/2017/03/30041-SMAP-File-Format-Specification-Sheet.pdf .
DOI: 10.6084/m9.figshare.13533148.v1
title: Additional file 1 of Oxytocin use in trial of labor after cesarean and its relationship with risk of uterine rupture in women with one previous cesarean section: a meta-analysis of observational studies

description: Additional file 1: Fig. S1. The pooled usage rate of oxytocin in spontaneous delivery group and induced labor group were 39.8% (95%CI: 0.532 to 0.682; p = 0.001; Pheterogeneity
DOI: 10.6084/m9.figshare.13533151.v1
title: Additional file 2 of Oxytocin use in trial of labor after cesarean and its relationship with risk of uterine rupture in women with one previous cesarean section: a meta-analysis of observational studies

description: Additional file 2: Fig. S2. The pooled rate of VBAC in spontaneous delivery group and induced labor group were 74.3% (95%CI: 0.679 to 0.807; p = 0.001; Pheterogeneity
DOI: 10.6084/m9.figshare.13533148
title: Additional file 1 of Oxytocin use in trial of labor after cesarean and its relationship with risk of uterine rupture in women with one previous cesarean section: a meta-analysis of observational studies

description: Additional file 1: Fig. S1. The pooled usage rate of oxytocin in spontaneous delivery group and induced labor group were 39.8% (95%CI: 0.532 to 0.682; p = 0.001; Pheterogeneity
DOI: 10.6084/m9.figshare.13533154.v1
title: Additional file 3 of Oxytocin use in trial of labor after cesarean and its relationship with risk of uterine rupture in women with one previous cesarean section: a meta-analysis of observational studies

description: Additional file 3: Fig. S3. The pooled rate of uterine rupture in spontaneous delivery group and induced labor group were 0.7% (95%CI: 0.004 to 0.009; p
DOI: 10.6084/m9.figshare.13533154
title: Additional file 3 of Oxytocin use in trial of labor after cesarean and its relationship with risk of uterine rupture in women with one previous cesarean section: a meta-analysis of observational studies

description: Additional file 3: Fig. S3. The pooled rate of uterine rupture in spontaneous delivery group and induced labor group were 0.7% (95%CI: 0.004 to 0.009; p
DOI: 10.6084/m9.figshare.13533157.v1
title: Additional file 4 of Oxytocin use in trial of labor after cesarean and its relationship with risk of uterine rupture in women with one previous cesarean section: a meta-analysis of observational studies

description: Additional file 4: Fig. S4. The sensitivity analysis by removing one study at the time to evaluate the weights of individual studies on the pooled SMDs. The result was relatively robust for the meta-analysis, with no reverse outcomes.
DOI: 10.6084/m9.figshare.13533151
title: Additional file 2 of Oxytocin use in trial of labor after cesarean and its relationship with risk of uterine rupture in women with one previous cesarean section: a meta-analysis of observational studies

description: Additional file 2: Fig. S2. The pooled rate of VBAC in spontaneous delivery group and induced labor group were 74.3% (95%CI: 0.679 to 0.807; p = 0.001; Pheterogeneity
DOI: 10.6084/m9.figshare.13533157
title: Additional file 4 of Oxytocin use in trial of labor after cesarean and its relationship with risk of uterine rupture in women with one previous cesarean section: a meta-analysis of observational studies

description: Additional file 4: Fig. S4. The sensitivity analysis by removing one study at the time to evaluate the weights of individual studies on the pooled SMDs. The result was relatively robust for the meta-analysis, with no reverse outcomes.
DOI: 10.6084/m9.figshare.13533160
title: Additional file 5 of Oxytocin use in trial of labor after cesarean and its relationship with risk of uterine rupture in women with one previous cesarean section: a meta-analysis of observational studies

description: Additional file 5: Fig. S5. Funnel plots and Egger’s test were used to reveal possible publication bias. The results showed a possible overestimation of effect size in the usage rate of oxytocin in spontaneous delivery (p = 0.048), the rate of uterine rupture in both spontaneous delivery (p = 0.031) and induction of labor.
DOI: 10.6084/m9.figshare.13533160.v1
title: Additional file 5 of Oxytocin use in trial of labor after cesarean and its relationship with risk of uterine rupture in women with one previous cesarean section: a meta-analysis of observational studies

description: Additional file 5: Fig. S5. Funnel plots and Egger’s test were used to reveal possible publication bias. The results showed a possible overestimation of effect size in the usage rate of oxytocin in spontaneous delivery (p = 0.048), the rate of uterine rupture in both spontaneous delivery (p = 0.031) and induction of labor.
DOI: 10.6084/m9.figshare.13533172.v1
title: Additional file 1 of DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome

description: Additional file 1: Table S1. Differentially methylated probes in PHMDS samples compared to controls. For each probe, listed are: methylation % difference, p value, adjusted p value, chromosome and chromosome position, and where available overlapping UCSC Gene name, UCSC gene type and UCSC CpG island.
DOI: 10.6084/m9.figshare.13533175
title: Additional file 2 of DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome

description: Additional file 2: Table S2. PHMDS and control sample information. Details for each sample listed include: age, sex, and the predicted cell type composition.
DOI: 10.6084/m9.figshare.13533172
title: Additional file 1 of DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome

description: Additional file 1: Table S1. Differentially methylated probes in PHMDS samples compared to controls. For each probe, listed are: methylation % difference, p value, adjusted p value, chromosome and chromosome position, and where available overlapping UCSC Gene name, UCSC gene type and UCSC CpG island.
DOI: 10.6084/m9.figshare.13533181.v1
title: Additional file 4 of DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome

description: Additional file 4: Table S3. PHMDS DMRs: Details for each DMR listed include: chromosome, start and end, width, number of CpGs, statistical significance (Stouffer and Fisher test), distance to nearest CpG island, distance to nearest gene and where available overlapping gene/s.
DOI: 10.6084/m9.figshare.13533175.v1
title: Additional file 2 of DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome

description: Additional file 2: Table S2. PHMDS and control sample information. Details for each sample listed include: age, sex, and the predicted cell type composition.
DOI: 10.6084/m9.figshare.13533181
title: Additional file 4 of DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome

description: Additional file 4: Table S3. PHMDS DMRs: Details for each DMR listed include: chromosome, start and end, width, number of CpGs, statistical significance (Stouffer and Fisher test), distance to nearest CpG island, distance to nearest gene and where available overlapping gene/s.
DOI: 10.6084/m9.figshare.13533187.v1
title: Additional file 6 of DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome

description: Additional file 6: Table S5. Statistical comparison of metabolite profiles. Results of the statistical comparisons for metabolite levels comparing control lymphoblastoid cell lines (LCLs) to the cell lines from individuals with small 22q13 deletions (
DOI: 10.6084/m9.figshare.13533187
title: Additional file 6 of DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome

description: Additional file 6: Table S5. Statistical comparison of metabolite profiles. Results of the statistical comparisons for metabolite levels comparing control lymphoblastoid cell lines (LCLs) to the cell lines from individuals with small 22q13 deletions (
DOI: 10.6084/m9.figshare.13533184
title: Additional file 5 of DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome

description: Additional file 5: Table S4. Metabolic profiling plates. Table includes listing of substrates in the individual wells of the metabolic profiling plates.
DOI: 10.6084/m9.figshare.13533184.v1
title: Additional file 5 of DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome

description: Additional file 5: Table S4. Metabolic profiling plates. Table includes listing of substrates in the individual wells of the metabolic profiling plates.
DOI: 10.6084/m9.figshare.13533200.v1
title: Additional file 5 of The apple MdCOP1-interacting protein 1 negatively regulates hypocotyl elongation and anthocyanin biosynthesis

description: Additional file 5: Fig. S1. The protein structure comparison of MdCIP1 and AtCIP1. Fig. S2. Identification of the MdCIP1-OX/cip1 Arabidopsis seedlings at the DNA level. Fig. S3. The coiled-coil region of MdCIP1 interacts with MdCOP1 in vitro pull-down assay. Fig. S4. MdCIP1 interacts with AtCOP1. Fig. S5. Identification of the MdCIP1-OX/cop1–4 Arabidopsis seedlings at the DNA level. Fig. S6. MdCIP1-OX/cop1–4 presents the cop1–4 phenotype at the adult stage.
DOI: 10.6084/m9.figshare.13533200
title: Additional file 5 of The apple MdCOP1-interacting protein 1 negatively regulates hypocotyl elongation and anthocyanin biosynthesis

description: Additional file 5: Fig. S1. The protein structure comparison of MdCIP1 and AtCIP1. Fig. S2. Identification of the MdCIP1-OX/cip1 Arabidopsis seedlings at the DNA level. Fig. S3. The coiled-coil region of MdCIP1 interacts with MdCOP1 in vitro pull-down assay. Fig. S4. MdCIP1 interacts with AtCOP1. Fig. S5. Identification of the MdCIP1-OX/cop1–4 Arabidopsis seedlings at the DNA level. Fig. S6. MdCIP1-OX/cop1–4 presents the cop1–4 phenotype at the adult stage.
DOI: 10.6084/m9.figshare.13533308.v1
title: Additional file 12 of Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary

description: Additional file 12: Table S2. Bray-Curtis beta-diversity summary statistics calculated using adonis2 Permutational Multivariate Analysis of Variance Using Distance Matrices test.
DOI: 10.6084/m9.figshare.13533314
title: Additional file 14 of Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary

description: Additional file 14: Table S4. Raw sequencing data accession information. This spreadsheet includes BioSample information for each oyster with corresponding Accession numbers for 16S rRNA gene amplicon or metatranscriptome files.
DOI: 10.6084/m9.figshare.13533308
title: Additional file 12 of Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary

description: Additional file 12: Table S2. Bray-Curtis beta-diversity summary statistics calculated using adonis2 Permutational Multivariate Analysis of Variance Using Distance Matrices test.
DOI: 10.6084/m9.figshare.13533314.v1
title: Additional file 14 of Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary

description: Additional file 14: Table S4. Raw sequencing data accession information. This spreadsheet includes BioSample information for each oyster with corresponding Accession numbers for 16S rRNA gene amplicon or metatranscriptome files.
DOI: 10.6084/m9.figshare.13533305
title: Additional file 11 of Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary

description: Additional file 11: Table S1. Sequencing summary statistics, including the number of reads that passed quality control (QC) in each 16S rRNA gene amplicon and metatranscriptomic sample. No metatranscriptomes were sequenced for water samples.
DOI: 10.6084/m9.figshare.13533311.v1
title: Additional file 13 of Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary

description: Additional file 13: Table S3. Taxa present in &gt; 80% of all samples in the 16S rRNA gene amplicon and metatranscriptomic datasets. This table corresponds to Fig. S6.
DOI: 10.6084/m9.figshare.13533305.v1
title: Additional file 11 of Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary

description: Additional file 11: Table S1. Sequencing summary statistics, including the number of reads that passed quality control (QC) in each 16S rRNA gene amplicon and metatranscriptomic sample. No metatranscriptomes were sequenced for water samples.
DOI: 10.6084/m9.figshare.13533311
title: Additional file 13 of Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary

description: Additional file 13: Table S3. Taxa present in &gt; 80% of all samples in the 16S rRNA gene amplicon and metatranscriptomic datasets. This table corresponds to Fig. S6.
DOI: 10.6084/m9.figshare.13533421.v1
title: Additional file 1 of Berry syndrome: a case report and literature review

description: Additional file 1. Literature review of 89 cases of Berry syndrome from 1982 to June 2019. The following clinical data were extracted and reviewed: sex, presence of clinical symptoms, premature birth, age at diagnosis, diagnostic methods, anomalies recognized by echocardiography, anatomic features of the cardiac anomalies (morphology of aortic artery, APW type, type of ductus arteriosus, and original site of RPA), associated cardiac and extracardiac anomalies, chromosomal abnormalities, age at surgery, types of surgery, postoperative details (postoperative hospitalization, postoperative follow-up time, postoperative complications, and reintervention after surgery), outcome, cause of death, preoperative and postoperative pulmonary artery pressure, and the presence of a massively dilated vascular sac.