cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11610615.v2
title: Additional file 6 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S4. Included brain tissue material. The brain sections processed in the study are listed together with the total number of cells segmented in each brain tissue and the average reads/cell for all detected targets. The ratio of expected reads indicates the quality filtering threshold set to obtain 95% or 96% expected reads out of total reads. The last column shows if the brain section was detected using the first or the second target panel of padlock probes.
DOI: 10.6084/m9.figshare.11610618.v1
title: Additional file 7: of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S5. Raw read counts E15. The raw read counts for the individual targets for each brain section and the selected regions after processing of the ISS image data.
DOI: 10.6084/m9.figshare.11610615.v1
title: Additional file 6: of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S4. Included brain tissue material. The brain sections processed in the study are listed together with the total number of cells segmented in each brain tissue and the average reads/cell for all detected targets. The ratio of expected reads indicates the quality filtering threshold set to obtain 95% or 96% expected reads out of total reads. The last column shows if the brain section was detected using the first or the second target panel of padlock probes.
DOI: 10.6084/m9.figshare.11610606
title: Additional file 5 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S3. Whole brain editing levels. The editing levels for the editing sites included in the analysis are shown as mean editing level for the included biological replicates for each developmental stage together with the standard deviation (SD).
DOI: 10.6084/m9.figshare.11610606.v2
title: Additional file 5 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S3. Whole brain editing levels. The editing levels for the editing sites included in the analysis are shown as mean editing level for the included biological replicates for each developmental stage together with the standard deviation (SD).
DOI: 10.6084/m9.figshare.11610606.v1
title: Additional file 5: of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S3. Whole brain editing levels. The editing levels for the editing sites included in the analysis are shown as mean editing level for the included biological replicates for each developmental stage together with the standard deviation (SD).
DOI: 10.6084/m9.figshare.11610594
title: MOESM3 of A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma

description: Additional file 3 Additional information to generate differentially expressed genes from ICGC database. This archive contains a SH script to filter dataset and a R script for data clustering and differential analysis
DOI: 10.6084/m9.figshare.11610594.v1
title: MOESM3 of A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma

description: Additional file 3 Additional information to generate differentially expressed genes from ICGC database. This archive contains a SH script to filter dataset and a R script for data clustering and differential analysis
DOI: 10.6084/m9.figshare.11610591
title: Additional file 2 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S2. Padlock probes used for ISS. The padlock probes of the target panel and their respective sequence (5′ to 3′). Bold, underlined nucleotides at the 3′ end target the edited site, underlined nucleotides mark the position of the barcodes, nucleotides in bold are target-specific sequences and nucleotides in Italic are the sequences complementary to fluorescently labeled detection probes. The last column shows the barcode change made for the updated target panel.
DOI: 10.6084/m9.figshare.11610585
title: MOESM2 of A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma

description: Additional file 2 Input data and results of the application of our pipeline regarding hepatocellular carcinoma progression. This archive contains input and output data related to hepatocellular carcinoma agressiveness that were used in this work to illustrate the benefits of our pipeline. The input data consists of differentially expressed genes (in CSV format) and the KEGG graph extraction (in SIF format). The output data consists in a Cytoscape session to explore the graph and the computational prediction results along with dynamic plots of the results (volcano plots, precision and stability studies, in HTML format).
DOI: 10.6084/m9.figshare.11610591.v2
title: Additional file 2 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S2. Padlock probes used for ISS. The padlock probes of the target panel and their respective sequence (5′ to 3′). Bold, underlined nucleotides at the 3′ end target the edited site, underlined nucleotides mark the position of the barcodes, nucleotides in bold are target-specific sequences and nucleotides in Italic are the sequences complementary to fluorescently labeled detection probes. The last column shows the barcode change made for the updated target panel.
DOI: 10.6084/m9.figshare.11610585.v1
title: MOESM2 of A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma

description: Additional file 2 Input data and results of the application of our pipeline regarding hepatocellular carcinoma progression. This archive contains input and output data related to hepatocellular carcinoma agressiveness that were used in this work to illustrate the benefits of our pipeline. The input data consists of differentially expressed genes (in CSV format) and the KEGG graph extraction (in SIF format). The output data consists in a Cytoscape session to explore the graph and the computational prediction results along with dynamic plots of the results (volcano plots, precision and stability studies, in HTML format).
DOI: 10.6084/m9.figshare.11610591.v1
title: Additional file 2: of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S2. Padlock probes used for ISS. The padlock probes of the target panel and their respective sequence (5′ to 3′). Bold, underlined nucleotides at the 3′ end target the edited site, underlined nucleotides mark the position of the barcodes, nucleotides in bold are target-specific sequences and nucleotides in Italic are the sequences complementary to fluorescently labeled detection probes. The last column shows the barcode change made for the updated target panel.
DOI: 10.6084/m9.figshare.11610582
title: Additional file 22 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S14. Microscope exposure times (in milli-seconds) for the different channels used for ISS.
DOI: 10.6084/m9.figshare.11610582.v2
title: Additional file 22 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S14. Microscope exposure times (in milli-seconds) for the different channels used for ISS.
DOI: 10.6084/m9.figshare.11610576
title: Additional file 21 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S13. Gene functions and editing categories. The gene functions found in literature and associated molecular processes from http://geneontology.org/ for the transcripts we analyzed and categorized by their spatial and cell-type-specific editing profile [33, 37, 39, 47–55]. The transcripts were classified as “Unregulated” when neither region-specific nor cell-type-specific editing could be found and “Regulated” when we observed differences in editing level between regions or between cell types. Unc80 was categorized as “Potentially regulated” based on the spatiotemporal editing patterns, but due to insufficient data statistical significance could not be shown for the observed patterns.
DOI: 10.6084/m9.figshare.11610582.v1
title: Additional file 22: of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S14. Microscope exposure times (in milli-seconds) for the different channels used for ISS.
DOI: 10.6084/m9.figshare.11610576.v2
title: Additional file 21 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S13. Gene functions and editing categories. The gene functions found in literature and associated molecular processes from http://geneontology.org/ for the transcripts we analyzed and categorized by their spatial and cell-type-specific editing profile [33, 37, 39, 47–55]. The transcripts were classified as “Unregulated” when neither region-specific nor cell-type-specific editing could be found and “Regulated” when we observed differences in editing level between regions or between cell types. Unc80 was categorized as “Potentially regulated” based on the spatiotemporal editing patterns, but due to insufficient data statistical significance could not be shown for the observed patterns.
DOI: 10.6084/m9.figshare.11610576.v1
title: Additional file 21: of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S13. Gene functions and editing categories. The gene functions found in literature and associated molecular processes from http://geneontology.org/ for the transcripts we analyzed and categorized by their spatial and cell-type-specific editing profile [33, 37, 39, 47–55]. The transcripts were classified as “Unregulated” when neither region-specific nor cell-type-specific editing could be found and “Regulated” when we observed differences in editing level between regions or between cell types. Unc80 was categorized as “Potentially regulated” based on the spatiotemporal editing patterns, but due to insufficient data statistical significance could not be shown for the observed patterns.
DOI: 10.6084/m9.figshare.11610564
title: Additional file 1 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S1. Selected editing sites for the study. The editing sites (transcript followed by editing site) included in the target panel are listed together with their observed editing profile during development (Editing profile), the potential alternative transcript names (Alternative name), how they were processed in the analysis (Status), how many replicates the editing site was covered by and the reference number of the sequence used for the design of the padlock probes.
DOI: 10.6084/m9.figshare.11610567
title: Additional file 20 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S12. Comparison of editing profiles for cells classified as Sst-positive interneurons, Pcp4-positive pyramidal neurons and Plp1-positive oligodendrocyte lineage at different developmental stages. The individual transcripts which were edited at different levels in the cell populations are listed together with the level of significance (Dunn-Sidak with correction for multiple testing).
DOI: 10.6084/m9.figshare.11610564.v2
title: Additional file 1 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S1. Selected editing sites for the study. The editing sites (transcript followed by editing site) included in the target panel are listed together with their observed editing profile during development (Editing profile), the potential alternative transcript names (Alternative name), how they were processed in the analysis (Status), how many replicates the editing site was covered by and the reference number of the sequence used for the design of the padlock probes.
DOI: 10.6084/m9.figshare.11610567.v2
title: Additional file 20 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S12. Comparison of editing profiles for cells classified as Sst-positive interneurons, Pcp4-positive pyramidal neurons and Plp1-positive oligodendrocyte lineage at different developmental stages. The individual transcripts which were edited at different levels in the cell populations are listed together with the level of significance (Dunn-Sidak with correction for multiple testing).
DOI: 10.6084/m9.figshare.11610564.v1
title: Additional file 1: of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S1. Selected editing sites for the study. The editing sites (transcript followed by editing site) included in the target panel are listed together with their observed editing profile during development (Editing profile), the potential alternative transcript names (Alternative name), how they were processed in the analysis (Status), how many replicates the editing site was covered by and the reference number of the sequence used for the design of the padlock probes.
DOI: 10.6084/m9.figshare.11610567.v1
title: Additional file 20: of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S12. Comparison of editing profiles for cells classified as Sst-positive interneurons, Pcp4-positive pyramidal neurons and Plp1-positive oligodendrocyte lineage at different developmental stages. The individual transcripts which were edited at different levels in the cell populations are listed together with the level of significance (Dunn-Sidak with correction for multiple testing).
DOI: 10.6084/m9.figshare.11610555
title: MOESM6 of DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing

description: Additional file 6. Table S6
DOI: 10.6084/m9.figshare.11610555.v1
title: MOESM6 of DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing

description: Additional file 6. Table S6
DOI: 10.6084/m9.figshare.11610549
title: MOESM5 of DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing

description: Additional file 5. Table S5
DOI: 10.6084/m9.figshare.11610549.v1
title: MOESM5 of DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing

description: Additional file 5. Table S5
DOI: 10.6084/m9.figshare.11610546
title: Additional file 17 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S11. Region-specific editing. The differences in regional editing found for individual editing sites at each developmental stage as well as between which regions the difference was found and at which level of significance (Dunn-Sidak with correction for multiple testing).
DOI: 10.6084/m9.figshare.11610546.v2
title: Additional file 17 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S11. Region-specific editing. The differences in regional editing found for individual editing sites at each developmental stage as well as between which regions the difference was found and at which level of significance (Dunn-Sidak with correction for multiple testing).
DOI: 10.6084/m9.figshare.11610543
title: MOESM4 of DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing

description: Additional file 4. Table S4
DOI: 10.6084/m9.figshare.11610543.v1
title: MOESM4 of DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing

description: Additional file 4. Table S4
DOI: 10.6084/m9.figshare.11610546.v1
title: Additional file 17: of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S11. Region-specific editing. The differences in regional editing found for individual editing sites at each developmental stage as well as between which regions the difference was found and at which level of significance (Dunn-Sidak with correction for multiple testing).
DOI: 10.6084/m9.figshare.11610537
title: MOESM3 of DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing

description: Additional file 3. Table S3
DOI: 10.6084/m9.figshare.11610537.v1
title: MOESM3 of DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing

description: Additional file 3. Table S3
DOI: 10.6084/m9.figshare.11610534
title: Additional file 15 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S10. Varying regional editing profiles. The differences in general editing profile found for the investigated regions for the different developmental stages together with the level of significance (Dunn-Sidak with correction for multiple testing). The region showing the lower or the higher editing activity in each comparison is also indicated.
DOI: 10.6084/m9.figshare.11610534.v2
title: Additional file 15 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S10. Varying regional editing profiles. The differences in general editing profile found for the investigated regions for the different developmental stages together with the level of significance (Dunn-Sidak with correction for multiple testing). The region showing the lower or the higher editing activity in each comparison is also indicated.
DOI: 10.6084/m9.figshare.11610534.v1
title: Additional file 15: of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S10. Varying regional editing profiles. The differences in general editing profile found for the investigated regions for the different developmental stages together with the level of significance (Dunn-Sidak with correction for multiple testing). The region showing the lower or the higher editing activity in each comparison is also indicated.
DOI: 10.6084/m9.figshare.11610519
title: Additional file 13 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S9. Correlation of editing levels to published data. The editing sites included in our analysis are listed with their respective derived editing level for whole brain and editing levels found in published studies together with the respective reference [21, 33, 44–46].
DOI: 10.6084/m9.figshare.11610519.v2
title: Additional file 13 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S9. Correlation of editing levels to published data. The editing sites included in our analysis are listed with their respective derived editing level for whole brain and editing levels found in published studies together with the respective reference [21, 33, 44–46].
DOI: 10.6084/m9.figshare.11610519.v1
title: Additional file 13: of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S9. Correlation of editing levels to published data. The editing sites included in our analysis are listed with their respective derived editing level for whole brain and editing levels found in published studies together with the respective reference [21, 33, 44–46].
DOI: 10.6084/m9.figshare.11610498
title: Additional file 10 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S8. Raw read counts adult. The raw read counts for the individual targets for each brain section and the selected regions after processing of the ISS image data.
DOI: 10.6084/m9.figshare.11610498.v1
title: Additional file 10: of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S8. Raw read counts adult. The raw read counts for the individual targets for each brain section and the selected regions after processing of the ISS image data.
DOI: 10.6084/m9.figshare.11610498.v2
title: Additional file 10 of Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

description: Table S8. Raw read counts adult. The raw read counts for the individual targets for each brain section and the selected regions after processing of the ISS image data.
DOI: 10.6084/m9.figshare.11610408
title: MOESM2 of Changes in the expression of genes encoding type IV pili-associated proteins are seen when Clostridium perfringens is grown in liquid or on surfaces

description: Additional file 2. Table S5.
DOI: 10.6084/m9.figshare.11610408.v1
title: MOESM2 of Changes in the expression of genes encoding type IV pili-associated proteins are seen when Clostridium perfringens is grown in liquid or on surfaces

description: Additional file 2. Table S5.
DOI: 10.6084/m9.figshare.11610387
title: MOESM7 of miRNA and circRNA expression patterns in mouse brain during toxoplasmosis development

description: Additional file 7: Table S5. Annotation for all circRNAs identified in this study.
DOI: 10.6084/m9.figshare.11610387.v1
title: MOESM7 of miRNA and circRNA expression patterns in mouse brain during toxoplasmosis development

description: Additional file 7: Table S5. Annotation for all circRNAs identified in this study.