cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26990398
title: Additional file 12 of Sex and age differences in social and cognitive function in offspring exposed to late gestational hypoxia

description: Additional file 12: Table S4. Comparison of gestational hypoxia parameters on social and cognitive offspring outcomes. SD Sprague–Dawley, GD gestational day.
DOI: 10.6084/m9.figshare.26990398.v1
title: Additional file 12 of Sex and age differences in social and cognitive function in offspring exposed to late gestational hypoxia

description: Additional file 12: Table S4. Comparison of gestational hypoxia parameters on social and cognitive offspring outcomes. SD Sprague–Dawley, GD gestational day.
DOI: 10.6084/m9.figshare.26990401
title: Additional file 1 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 1: Genotyping and RT-qPCR primers. Contains the genotyping primer sequences A and RT-qPCR TaqMan gene expression assays B used.
DOI: 10.6084/m9.figshare.26990401.v1
title: Additional file 1 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 1: Genotyping and RT-qPCR primers. Contains the genotyping primer sequences A and RT-qPCR TaqMan gene expression assays B used.
DOI: 10.6084/m9.figshare.26990404
title: Additional file 2 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 2: Cell type-specific gene lists. Contains lists of neuronal, astrocytic, microglial, oligodendrocytic, and endothelial cell-specific genes
DOI: 10.6084/m9.figshare.26990404.v1
title: Additional file 2 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 2: Cell type-specific gene lists. Contains lists of neuronal, astrocytic, microglial, oligodendrocytic, and endothelial cell-specific genes
DOI: 10.6084/m9.figshare.26990407
title: Additional file 3 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 3: Figure 2 additional information. Contains Pos vs Input fold change for each cell type specific gene (Additional file 2) from Camk2a-NuTRAP TRAP-isolated RNA-seq A, CIBERSORTx results B, Pos vs Input enriched genes C, Pos vs Input depleted genes D, GO biological processes of enriched genes E, IPA functions of enriched genes F, GO biological processes of depleted genes G, and IPA functions of depleted genes H.
DOI: 10.6084/m9.figshare.26990407.v1
title: Additional file 3 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 3: Figure 2 additional information. Contains Pos vs Input fold change for each cell type specific gene (Additional file 2) from Camk2a-NuTRAP TRAP-isolated RNA-seq A, CIBERSORTx results B, Pos vs Input enriched genes C, Pos vs Input depleted genes D, GO biological processes of enriched genes E, IPA functions of enriched genes F, GO biological processes of depleted genes G, and IPA functions of depleted genes H.
DOI: 10.6084/m9.figshare.26990410
title: Additional file 4 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 4: MiSeq CEGXQC reports. Contains CEGXQC reports from the initial MiSeq run performed to assess library quality and conversion efficiency. BS and oxBS reports for each sample are found under the same tab in the following order: 389Input, 389Neg, 389Pos, 391Input, 391Neg, 391Pos, 392Input, 392Neg, 392Pos, 396Input, 396Neg, 396Pos.
DOI: 10.6084/m9.figshare.26990410.v1
title: Additional file 4 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 4: MiSeq CEGXQC reports. Contains CEGXQC reports from the initial MiSeq run performed to assess library quality and conversion efficiency. BS and oxBS reports for each sample are found under the same tab in the following order: 389Input, 389Neg, 389Pos, 391Input, 391Neg, 391Pos, 392Input, 392Neg, 392Pos, 396Input, 396Neg, 396Pos.
DOI: 10.6084/m9.figshare.26990413
title: Additional file 5 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 5: NovaSeq 6000 FastQC reports. Contains FastQC reports from the NovaSeq 6000 run performed to obtain deeper sequencing on the Input and Positive fraction. BS and oxBS reports for each sample are found under the same tab in the following order: 389Input, 389Pos, 391Input, 391Pos, 392Input, 392Pos, 396Input, 396Pos.
DOI: 10.6084/m9.figshare.26990413.v1
title: Additional file 5 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 5: NovaSeq 6000 FastQC reports. Contains FastQC reports from the NovaSeq 6000 run performed to obtain deeper sequencing on the Input and Positive fraction. BS and oxBS reports for each sample are found under the same tab in the following order: 389Input, 389Pos, 391Input, 391Pos, 392Input, 392Pos, 396Input, 396Pos.
DOI: 10.6084/m9.figshare.26990416.v1
title: Additional file 6 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 6: DMCGR motifs. Known HOMER motifs enriched in hyper Astrocyte vs Neuron A, hypo Astrocyte vs Neuron B, hyper Microglia vs Neuron C, hypo Microglia vs Neuron D, hyper Astrocyte vs Microglia E, and hypo Astrocyte vs Microglia DMCGRs.
DOI: 10.6084/m9.figshare.26990416
title: Additional file 6 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 6: DMCGR motifs. Known HOMER motifs enriched in hyper Astrocyte vs Neuron A, hypo Astrocyte vs Neuron B, hyper Microglia vs Neuron C, hypo Microglia vs Neuron D, hyper Astrocyte vs Microglia E, and hypo Astrocyte vs Microglia DMCGRs.
DOI: 10.6084/m9.figshare.26990419
title: Additional file 7 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 7: DhMCGR motifs. Known HOMER motifs enriched in hyper Astrocyte vs Neuron A, hypo Astrocyte vs Neuron B, hyper Microglia vs Neuron C, hypo Microglia vs Neuron D, hyper Astrocyte vs Microglia E, and hypo Astrocyte vs Microglia DhMCGRs.
DOI: 10.6084/m9.figshare.26990419.v1
title: Additional file 7 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 7: DhMCGR motifs. Known HOMER motifs enriched in hyper Astrocyte vs Neuron A, hypo Astrocyte vs Neuron B, hyper Microglia vs Neuron C, hypo Microglia vs Neuron D, hyper Astrocyte vs Microglia E, and hypo Astrocyte vs Microglia DhMCGRs.
DOI: 10.6084/m9.figshare.26990422
title: Additional file 8 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 8: DMCHR motifs. Known HOMER motifs enriched in hyper Astrocyte vs Neuron A, hypo Astrocyte vs Neuron B, hyper Microglia vs Neuron C, hypo Microglia vs Neuron D, hyper Astrocyte vs Microglia E, and hypo Astrocyte vs Microglia DMCHRs
DOI: 10.6084/m9.figshare.26990422.v1
title: Additional file 8 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 8: DMCHR motifs. Known HOMER motifs enriched in hyper Astrocyte vs Neuron A, hypo Astrocyte vs Neuron B, hyper Microglia vs Neuron C, hypo Microglia vs Neuron D, hyper Astrocyte vs Microglia E, and hypo Astrocyte vs Microglia DMCHRs
DOI: 10.6084/m9.figshare.26990425
title: Additional file 9 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 9: Genes by expression level in neurons, astrocytes, and microglia. Contains genes by expression level (high, mid, low, and non-expressed) for neurons A, astrocytes B, and microglia C.
DOI: 10.6084/m9.figshare.26990425.v1
title: Additional file 9 of Differential usage of DNA modifications in neurons, astrocytes, and microglia

description: Additional file 9: Genes by expression level in neurons, astrocytes, and microglia. Contains genes by expression level (high, mid, low, and non-expressed) for neurons A, astrocytes B, and microglia C.
DOI: 10.6084/m9.figshare.26990434
title: Additional file 2 of Inhibition of exosome biogenesis affects cell motility in heterogeneous sub-populations of paediatric-type diffuse high-grade gliomas

description: Additional file 2: Gene signatures associated with OPBG-DIPG002 2B4 derived-clone and OPBGGBM0025E2 derived-clone.
DOI: 10.6084/m9.figshare.26990434.v1
title: Additional file 2 of Inhibition of exosome biogenesis affects cell motility in heterogeneous sub-populations of paediatric-type diffuse high-grade gliomas

description: Additional file 2: Gene signatures associated with OPBG-DIPG002 2B4 derived-clone and OPBGGBM0025E2 derived-clone.
DOI: 10.6084/m9.figshare.26990437
title: Additional file 3 of Inhibition of exosome biogenesis affects cell motility in heterogeneous sub-populations of paediatric-type diffuse high-grade gliomas

description: Additional file 3: Summary of the proteomic Label-Free Quantitation (LFQ) analysis performed for theclones 2B4, 5E2, 1C5, and 1D3 based on the comparison of mono versus coculture conditions.
DOI: 10.6084/m9.figshare.26990437.v1
title: Additional file 3 of Inhibition of exosome biogenesis affects cell motility in heterogeneous sub-populations of paediatric-type diffuse high-grade gliomas

description: Additional file 3: Summary of the proteomic Label-Free Quantitation (LFQ) analysis performed for theclones 2B4, 5E2, 1C5, and 1D3 based on the comparison of mono versus coculture conditions.
DOI: 10.6084/m9.figshare.26990500
title: Additional file 1 of Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

description: Additional file 1: Table S1. Collection and assembly information of 12 Justicia species
DOI: 10.6084/m9.figshare.26990500.v1
title: Additional file 1 of Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

description: Additional file 1: Table S1. Collection and assembly information of 12 Justicia species
DOI: 10.6084/m9.figshare.26990503
title: Additional file 2 of Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

description: Additional file 2: Table S2. All the GenBank accession numbers used for phylogenetic analyses utilized in our study
DOI: 10.6084/m9.figshare.26990503.v1
title: Additional file 2 of Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

description: Additional file 2: Table S2. All the GenBank accession numbers used for phylogenetic analyses utilized in our study
DOI: 10.6084/m9.figshare.26990506
title: Additional file 3 of Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

description: Additional file 3: Table S3. Gene sizes of all the protein-coding genes of 13 Justicia chloroplast genomes
DOI: 10.6084/m9.figshare.26990506.v1
title: Additional file 3 of Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

description: Additional file 3: Table S3. Gene sizes of all the protein-coding genes of 13 Justicia chloroplast genomes
DOI: 10.6084/m9.figshare.26990509
title: Additional file 4 of Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

description: Additional file 4: Table S4. Genes with introns in the 13 Justicia chloroplast genomes, including the exon and intron lengths
DOI: 10.6084/m9.figshare.26990509.v1
title: Additional file 4 of Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

description: Additional file 4: Table S4. Genes with introns in the 13 Justicia chloroplast genomes, including the exon and intron lengths
DOI: 10.6084/m9.figshare.26990512
title: Additional file 5 of Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

description: Additional file 5: Table S5. Codon usage bias of 20 amino acids within 13 Justicia chloroplast genomes
DOI: 10.6084/m9.figshare.26990512.v1
title: Additional file 5 of Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

description: Additional file 5: Table S5. Codon usage bias of 20 amino acids within 13 Justicia chloroplast genomes
DOI: 10.6084/m9.figshare.26990515
title: Additional file 6 of Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

description: Additional file 6: Table S6. Quantity statistics of SSRs of the 13 Justicia chloroplast genomes
DOI: 10.6084/m9.figshare.26990515.v1
title: Additional file 6 of Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

description: Additional file 6: Table S6. Quantity statistics of SSRs of the 13 Justicia chloroplast genomes
DOI: 10.6084/m9.figshare.26990548
title: Additional file 3 of Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections

description: Additional file 3: Supplementary File 1. Lists of differentially expressed genes (DEGs) from comparisons of symptomatic and asymptomatic HCMV infections to control samples, from GEO2R analysis of BioProject dataset PRJNA422858 ( https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE108211 ). Sheets A, B and C show GEO2R lists of DEGs from symptomatic vs control, asymptomatic vs control, and symptomatic vs asymptomatic HCMV samples comparisons. Sheets D and E show results of Reactome pathways overrepresentation analyses for significant (FDR &lt;= 0.05) DEGs from symptomatic vs control and asymptomatic vs control HCMV samples. Only pathways with entities FDR &lt; 0.05 are shown.
DOI: 10.6084/m9.figshare.26990548.v1
title: Additional file 3 of Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections

description: Additional file 3: Supplementary File 1. Lists of differentially expressed genes (DEGs) from comparisons of symptomatic and asymptomatic HCMV infections to control samples, from GEO2R analysis of BioProject dataset PRJNA422858 ( https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE108211 ). Sheets A, B and C show GEO2R lists of DEGs from symptomatic vs control, asymptomatic vs control, and symptomatic vs asymptomatic HCMV samples comparisons. Sheets D and E show results of Reactome pathways overrepresentation analyses for significant (FDR &lt;= 0.05) DEGs from symptomatic vs control and asymptomatic vs control HCMV samples. Only pathways with entities FDR &lt; 0.05 are shown.
DOI: 10.6084/m9.figshare.26990551
title: Additional file 4 of Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections

description: Additional file 4: Supplementary File 2. List of DESeq2 (Love et al., 2014) differential expression analysis results for gene counts from ballgown, including log2 fold change values and p values for expression changes in each gene for (A) MCMV vs control, (B) ZIKV vs control (PRJNA487357), (C) ZIKV vs control (PRJNA358758), (D) ZIKV FSS13205 vs control hiNPC, (E) ZIKV PE243 vs control hiNPC, and (F) ZIKV PE243 vs FSS13205 samples.
DOI: 10.6084/m9.figshare.26990551.v1
title: Additional file 4 of Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections

description: Additional file 4: Supplementary File 2. List of DESeq2 (Love et al., 2014) differential expression analysis results for gene counts from ballgown, including log2 fold change values and p values for expression changes in each gene for (A) MCMV vs control, (B) ZIKV vs control (PRJNA487357), (C) ZIKV vs control (PRJNA358758), (D) ZIKV FSS13205 vs control hiNPC, (E) ZIKV PE243 vs control hiNPC, and (F) ZIKV PE243 vs FSS13205 samples.
DOI: 10.6084/m9.figshare.26990554
title: Additional file 5 of Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections

description: Additional file 5: Supplementary File 3. List of DESeq2 (Love et al., 2014) differential expression analysis results for transcript counts from ballgown, including log2 fold change values and p values for expression changes in each transcript for (A) MCMV vs control, (B) ZIKV vs control (PRJNA487357), (C) ZIKV vs control (PRJNA358758), (D) ZIKV FSS13205 vs control hiNPC, (E) ZIKV PE243 vs control hiNPC, and (F) ZIKV PE243 vs FSS13205 samples.
DOI: 10.6084/m9.figshare.26990569
title: Additional file 10 of Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections

description: Additional file 10: Supplementary File 8. (A) Characteristics of 1276 editing sites from ZIKV and control samples. List of ADAR edited sites (identified via chromosome (CHR) and position (POS)) and individual nucleotide counts from ZIKV infections and control samples (PRJNA358758). (B) Characteristics of 148 significantly different editing sites between ZIKV and control samples. List of ADAR edited sites (identified via chromosome (CHR) and position (POS)) and average editing rates from ZIKV infections and control samples (PRJNA358758).
DOI: 10.6084/m9.figshare.26990569.v1
title: Additional file 10 of Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections

description: Additional file 10: Supplementary File 8. (A) Characteristics of 1276 editing sites from ZIKV and control samples. List of ADAR edited sites (identified via chromosome (CHR) and position (POS)) and individual nucleotide counts from ZIKV infections and control samples (PRJNA358758). (B) Characteristics of 148 significantly different editing sites between ZIKV and control samples. List of ADAR edited sites (identified via chromosome (CHR) and position (POS)) and average editing rates from ZIKV infections and control samples (PRJNA358758).
DOI: 10.6084/m9.figshare.26990572
title: Additional file 11 of Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections

description: Additional file 11: Supplementary File 9. Results of MAJIQ and VOILA analysis of editing sites from ZIKV and control samples (PRJNA358758). (A) Results of MAJIQ analysis of editing sites from ZIKV and control samples (PRJNA358758), with PSI/dPSI information for all LSVs identified. (B) Results of VOILA analysis of editing sites from ZIKV and control samples (PRJNA358758), with significant LSVs (|dPSI| &gt; 0.2 and p &lt; 0.05). (C) Information for LSVs in genes identified as Nova1 targets (Zhang et al., 2010).
DOI: 10.6084/m9.figshare.26990572.v1
title: Additional file 11 of Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections

description: Additional file 11: Supplementary File 9. Results of MAJIQ and VOILA analysis of editing sites from ZIKV and control samples (PRJNA358758). (A) Results of MAJIQ analysis of editing sites from ZIKV and control samples (PRJNA358758), with PSI/dPSI information for all LSVs identified. (B) Results of VOILA analysis of editing sites from ZIKV and control samples (PRJNA358758), with significant LSVs (|dPSI| &gt; 0.2 and p &lt; 0.05). (C) Information for LSVs in genes identified as Nova1 targets (Zhang et al., 2010).
DOI: 10.6084/m9.figshare.26990554.v1
title: Additional file 5 of Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections

description: Additional file 5: Supplementary File 3. List of DESeq2 (Love et al., 2014) differential expression analysis results for transcript counts from ballgown, including log2 fold change values and p values for expression changes in each transcript for (A) MCMV vs control, (B) ZIKV vs control (PRJNA487357), (C) ZIKV vs control (PRJNA358758), (D) ZIKV FSS13205 vs control hiNPC, (E) ZIKV PE243 vs control hiNPC, and (F) ZIKV PE243 vs FSS13205 samples.
DOI: 10.6084/m9.figshare.26990557
title: Additional file 6 of Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections

description: Additional file 6: Supplementary File 4. Alu editing index (AEI) values from the RNA Editing Indexer method (Roth et al., 2019) for (A) the PRJEB38849 MCMV dataset, (B) the ZIKV PRJNA487357 dataset, (C) the ZIKV PRJNA358758 dataset, and (D) the hiNPC ZIKV PRJNA551246 dataset. This includes quantifications of the ratio of A-to-G mismatches to total A reads (effectively the percent of As edited to Gs) in Alu repeat elements in humans or SINE B1/B2 repeat elements in mice, as well as the same metric for other variant types. A-to-G editing index serves as a general metric of transcriptome-wide levels of hyperediting, which primarily occur in repeat regions. Quantification of other variants serve as a measure of background noise, with the next most common modification type being C-to-T editing.
DOI: 10.6084/m9.figshare.26990557.v1
title: Additional file 6 of Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections

description: Additional file 6: Supplementary File 4. Alu editing index (AEI) values from the RNA Editing Indexer method (Roth et al., 2019) for (A) the PRJEB38849 MCMV dataset, (B) the ZIKV PRJNA487357 dataset, (C) the ZIKV PRJNA358758 dataset, and (D) the hiNPC ZIKV PRJNA551246 dataset. This includes quantifications of the ratio of A-to-G mismatches to total A reads (effectively the percent of As edited to Gs) in Alu repeat elements in humans or SINE B1/B2 repeat elements in mice, as well as the same metric for other variant types. A-to-G editing index serves as a general metric of transcriptome-wide levels of hyperediting, which primarily occur in repeat regions. Quantification of other variants serve as a measure of background noise, with the next most common modification type being C-to-T editing.
DOI: 10.6084/m9.figshare.26990575
title: Additional file 12 of Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections

description: Additional file 12: Supplementary File 10. (A) Characteristics of 1355 editing sites from ZIKV and control samples (PRJNA551246). List of ADAR edited sites (identified via chromosome (CHR) and position (POS)) and individual nucleotide counts from ZIKV infections with Cambodian (FSS13025) and Brazilian ZIKV (PE243) strains and control samples. (B) Characteristics of 9 significantly different editing sites between ZIKV and control samples (PRJNA551246). List of ADAR edited sites (identified via chromosome (CHR) and position (POS)), and average editing rates from ZIKV infections with Cambodian (FSS13025) and Brazilian ZIKV (PE243) strains and control samples.
DOI: 10.6084/m9.figshare.26990575.v1
title: Additional file 12 of Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections

description: Additional file 12: Supplementary File 10. (A) Characteristics of 1355 editing sites from ZIKV and control samples (PRJNA551246). List of ADAR edited sites (identified via chromosome (CHR) and position (POS)) and individual nucleotide counts from ZIKV infections with Cambodian (FSS13025) and Brazilian ZIKV (PE243) strains and control samples. (B) Characteristics of 9 significantly different editing sites between ZIKV and control samples (PRJNA551246). List of ADAR edited sites (identified via chromosome (CHR) and position (POS)), and average editing rates from ZIKV infections with Cambodian (FSS13025) and Brazilian ZIKV (PE243) strains and control samples.
DOI: 10.6084/m9.figshare.26990578
title: Additional file 13 of Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections

description: Additional file 13: Supplementary File 11. SubmiRine (Maxwell et al., 2015) results predicting differences in miRNA binding between unedited and edited transcripts. While no editing was found to alter miRNA binding in the MCMV or hiNPC ZIKV datasets, editing sites with potential links to changes in miRNA targeting were detected in 2 genes for the mouse ZIKV PRJNA487357 dataset and 26 genes for the mouse ZIKV PRJNA358758 dataset.