cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.15145688.v1
title: Additional file 6 of SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3′ tag-based RNA-seq of single cells

description: Additional file 6: Table S5. List of intronic PASs identified by SCAPTURE in six PBMC scRNA-seq datasets from 10x Genomics. SCAPTURE-identified intronic PASs in each PBMC sample were individually listed. (Related Fig. S5B).
DOI: 10.6084/m9.figshare.15145691
title: Additional file 7 of SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3′ tag-based RNA-seq of single cells

description: Additional file 7: Table S6. List of PASs identified by Sierra in six PBMC scRNA-seq datasets from 10x Genomics. Sierra-identified exonic and intronic PASs in each PBMC dataset were individually listed. (Related Fig. 3d and S6C).
DOI: 10.6084/m9.figshare.15145694
title: Additional file 8 of SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3′ tag-based RNA-seq of single cells

description: Additional file 8: Table S7. List of PASs identified by scAPA in six PBMC scRNA-seq datasets from 10x Genomics. scAPA-identified exonic and intronic PASs in each PBMC dataset were individually listed. (Related Fig. 3d and S6C).
DOI: 10.6084/m9.figshare.15145697
title: Additional file 9 of SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3′ tag-based RNA-seq of single cells

description: Additional file 9: Table S8. List of barcode, sample and cell type information of each single cell by DGE and DTE analyses in six PBMC scRNA-seq datasets from 10x Genomics. (Related Fig. 4f and S9A-C).
DOI: 10.6084/m9.figshare.15145694.v1
title: Additional file 8 of SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3′ tag-based RNA-seq of single cells

description: Additional file 8: Table S7. List of PASs identified by scAPA in six PBMC scRNA-seq datasets from 10x Genomics. scAPA-identified exonic and intronic PASs in each PBMC dataset were individually listed. (Related Fig. 3d and S6C).
DOI: 10.6084/m9.figshare.15145697.v1
title: Additional file 9 of SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3′ tag-based RNA-seq of single cells

description: Additional file 9: Table S8. List of barcode, sample and cell type information of each single cell by DGE and DTE analyses in six PBMC scRNA-seq datasets from 10x Genomics. (Related Fig. 4f and S9A-C).
DOI: 10.6084/m9.figshare.15145703
title: Additional file 1 of Negative SARS-CoV-2 PCR or rapid antigen test result and the subsequent risk of being infectious: a mathematical simulation study

description: Additional file 1. R-code of the Monte Carlo simulation model.
DOI: 10.6084/m9.figshare.15145703.v1
title: Additional file 1 of Negative SARS-CoV-2 PCR or rapid antigen test result and the subsequent risk of being infectious: a mathematical simulation study

description: Additional file 1. R-code of the Monte Carlo simulation model.
DOI: 10.6084/m9.figshare.15145788
title: Additional file 1 of From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon

description: Additional file 1. List of genes whose functional categories were analysed using GO enrichment.
DOI: 10.6084/m9.figshare.15145788.v1
title: Additional file 1 of From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon

description: Additional file 1. List of genes whose functional categories were analysed using GO enrichment.
DOI: 10.6084/m9.figshare.15145847
title: Additional file 1 of Quantifying and communicating the burden of COVID-19

description: Additional file 1.
DOI: 10.6084/m9.figshare.15145847.v1
title: Additional file 1 of Quantifying and communicating the burden of COVID-19

description: Additional file 1.
DOI: 10.6084/m9.figshare.15145850
title: Additional file 2 of Quantifying and communicating the burden of COVID-19

description: Additional file 2.
DOI: 10.6084/m9.figshare.15145850.v1
title: Additional file 2 of Quantifying and communicating the burden of COVID-19

description: Additional file 2.
DOI: 10.6084/m9.figshare.15145877
title: Additional file 2 of Transfer learning between preclinical models and human tumors identifies a conserved NK cell activation signature in anti-CTLA-4 responsive tumors

description: Additional file 2: Table S1. CoGAPS 21 pattern matrix with pattern weights for each cell. Table S2. FDR adjusted gene set statistics for all 21 CoGAPS patterns. Table S3. Differentially expressed genes across pseudotime in NK cells collected from tumors treated with anti-CTLA-4. Table S4. Correlation values and p-values for each of the 21 CoGAPS patterns and the CIBERSORT NK cell activation signature. Table S5. Correlation values and p-values for CIBERSORT cell type estimation and CTLA-4 expression in tumors from TCGA.
DOI: 10.6084/m9.figshare.15145877.v1
title: Additional file 2 of Transfer learning between preclinical models and human tumors identifies a conserved NK cell activation signature in anti-CTLA-4 responsive tumors

description: Additional file 2: Table S1. CoGAPS 21 pattern matrix with pattern weights for each cell. Table S2. FDR adjusted gene set statistics for all 21 CoGAPS patterns. Table S3. Differentially expressed genes across pseudotime in NK cells collected from tumors treated with anti-CTLA-4. Table S4. Correlation values and p-values for each of the 21 CoGAPS patterns and the CIBERSORT NK cell activation signature. Table S5. Correlation values and p-values for CIBERSORT cell type estimation and CTLA-4 expression in tumors from TCGA.
DOI: 10.6084/m9.figshare.15145881
title: Additional file 10 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 10: Table S10. Analysis of differentially expressed genes (DEG) for the milk type main effect. DEG are highlighted in blue. Genes colored gray were filtered out for being significant for the milk type x parity interaction or for having |log2 fold change|
DOI: 10.6084/m9.figshare.15145881.v1
title: Additional file 10 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 10: Table S10. Analysis of differentially expressed genes (DEG) for the milk type main effect. DEG are highlighted in blue. Genes colored gray were filtered out for being significant for the milk type x parity interaction or for having |log2 fold change|
DOI: 10.6084/m9.figshare.15145884
title: Additional file 11 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 11: Table S11. Gene ontology (GO) term and pathway analysis for the milk type main effect. Biological process (BP), molecular function (MF), cellular component (CC), and KEGG pathway results are shown in separate tabs.
DOI: 10.6084/m9.figshare.15145884.v1
title: Additional file 11 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 11: Table S11. Gene ontology (GO) term and pathway analysis for the milk type main effect. Biological process (BP), molecular function (MF), cellular component (CC), and KEGG pathway results are shown in separate tabs.
DOI: 10.6084/m9.figshare.15145887.v1
title: Additional file 12 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 12: Table S12. Milk type DEG associated with various immune response GO terms. GO terms are given in separate tabs. DEG associated with the GO term and their log2 fold changes (milk vs colostrum) are shown.
DOI: 10.6084/m9.figshare.15145887
title: Additional file 12 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 12: Table S12. Milk type DEG associated with various immune response GO terms. GO terms are given in separate tabs. DEG associated with the GO term and their log2 fold changes (milk vs colostrum) are shown.
DOI: 10.6084/m9.figshare.15145893
title: Additional file 1 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 1: Table S1. Sequencing statistics. Number of raw sequence reads, number of reads mapping to the S. scrofa 11.1 genome assembly, and percentage of mapped reads for each of the sequenced libraries.
DOI: 10.6084/m9.figshare.15145896
title: Additional file 2 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 2: Table S2. Summary of reads mapping to RNA regions of the swine genome. Number of raw sequence reads mapping to annotated RNA regions in the S. scrofa 11.1 genome assembly. RNA classifications are based on the NCBI S. scrofa annotation (Release 106).
DOI: 10.6084/m9.figshare.15145896.v1
title: Additional file 2 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 2: Table S2. Summary of reads mapping to RNA regions of the swine genome. Number of raw sequence reads mapping to annotated RNA regions in the S. scrofa 11.1 genome assembly. RNA classifications are based on the NCBI S. scrofa annotation (Release 106).
DOI: 10.6084/m9.figshare.15145902
title: Additional file 4 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 4: Table S4. Novel mRNA annotation. Annotation is given in GTF format.
DOI: 10.6084/m9.figshare.15145893.v1
title: Additional file 1 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 1: Table S1. Sequencing statistics. Number of raw sequence reads, number of reads mapping to the S. scrofa 11.1 genome assembly, and percentage of mapped reads for each of the sequenced libraries.
DOI: 10.6084/m9.figshare.15145899
title: Additional file 3 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 3: Table S3. Novel lncRNA annotation. Annotation is given in GTF format. LincRNA denotes intergenic lncRNA, ilncRNA denotes intronic RNA, lncNAT denotes natural antisense lncRNA, and isolncRNA denotes novel isoform lncRNA.
DOI: 10.6084/m9.figshare.15145899.v1
title: Additional file 3 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 3: Table S3. Novel lncRNA annotation. Annotation is given in GTF format. LincRNA denotes intergenic lncRNA, ilncRNA denotes intronic RNA, lncNAT denotes natural antisense lncRNA, and isolncRNA denotes novel isoform lncRNA.
DOI: 10.6084/m9.figshare.15145902.v1
title: Additional file 4 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 4: Table S4. Novel mRNA annotation. Annotation is given in GTF format.
DOI: 10.6084/m9.figshare.15145905.v1
title: Additional file 5 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 5: Table S5. BLAST search results for novel lncRNA against NONCODE databases. BLAST hits for novel lncRNA searched against NONCODE databases for multiple species. Entries in the species column indicate the top BLAST hit for the transcript in the given species.
DOI: 10.6084/m9.figshare.15145911
title: Additional file 7 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 7: Table S7. Analysis of differentially expressed transcripts (DET) for the milk type main effect. DET are highlighted in blue. Transcripts colored gray were filtered out for being significant for the milk type x parity interaction or for having |log2 fold change|
DOI: 10.6084/m9.figshare.15145911.v1
title: Additional file 7 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 7: Table S7. Analysis of differentially expressed transcripts (DET) for the milk type main effect. DET are highlighted in blue. Transcripts colored gray were filtered out for being significant for the milk type x parity interaction or for having |log2 fold change|
DOI: 10.6084/m9.figshare.15145905
title: Additional file 5 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 5: Table S5. BLAST search results for novel lncRNA against NONCODE databases. BLAST hits for novel lncRNA searched against NONCODE databases for multiple species. Entries in the species column indicate the top BLAST hit for the transcript in the given species.
DOI: 10.6084/m9.figshare.15145908
title: Additional file 6 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 6: Table S6. Analysis of differentially expressed transcripts (DET) for the milk type x parity interaction. DET are highlighted in blue.
DOI: 10.6084/m9.figshare.15145914.v1
title: Additional file 8 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 8: Table S8. Analysis of differentially expressed transcripts (DET) for the parity main effect. DET are highlighted in blue. Transcripts colored gray were filtered out for being significant for the milk type x parity interaction.
DOI: 10.6084/m9.figshare.15145908.v1
title: Additional file 6 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 6: Table S6. Analysis of differentially expressed transcripts (DET) for the milk type x parity interaction. DET are highlighted in blue.
DOI: 10.6084/m9.figshare.15145914
title: Additional file 8 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 8: Table S8. Analysis of differentially expressed transcripts (DET) for the parity main effect. DET are highlighted in blue. Transcripts colored gray were filtered out for being significant for the milk type x parity interaction.
DOI: 10.6084/m9.figshare.15145917
title: Additional file 9 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 9: Table S9. Analysis of differentially expressed genes (DEG) for the milk type x parity interaction. DEG are highlighted in blue.
DOI: 10.6084/m9.figshare.15145917.v1
title: Additional file 9 of Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

description: Additional file 9: Table S9. Analysis of differentially expressed genes (DEG) for the milk type x parity interaction. DEG are highlighted in blue.
DOI: 10.6084/m9.figshare.15145932
title: Additional file 11 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 11 : Table S9. mRNA nuclear export analysis in patient-derived neurons.
DOI: 10.6084/m9.figshare.15145932.v1
title: Additional file 11 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 11 : Table S9. mRNA nuclear export analysis in patient-derived neurons.
DOI: 10.6084/m9.figshare.15145941
title: Additional file 14 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 14 : Table S11. Gene ontology analysis in Drosophila
DOI: 10.6084/m9.figshare.15145938
title: Additional file 13 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 13 : Table S10. Differentially-expressed transcripts in Drosophila
DOI: 10.6084/m9.figshare.15145938.v1
title: Additional file 13 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 13 : Table S10. Differentially-expressed transcripts in Drosophila
DOI: 10.6084/m9.figshare.15145941.v1
title: Additional file 14 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 14 : Table S11. Gene ontology analysis in Drosophila
DOI: 10.6084/m9.figshare.15145950
title: Additional file 17 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 17 : Table S12. C9ORF72-ALS disease-modifying gene expression signature.
DOI: 10.6084/m9.figshare.15145950.v1
title: Additional file 17 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 17 : Table S12. C9ORF72-ALS disease-modifying gene expression signature.
DOI: 10.6084/m9.figshare.15145953.v1
title: Additional file 18 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 18 : Table S13. Conserved human-fly gene expression changes.
DOI: 10.6084/m9.figshare.15145953
title: Additional file 18 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 18 : Table S13. Conserved human-fly gene expression changes.
DOI: 10.6084/m9.figshare.15145977.v1
title: Additional file 2 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 2 : Table S1. RNA-seq statistics.
DOI: 10.6084/m9.figshare.15145977
title: Additional file 2 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 2 : Table S1. RNA-seq statistics.
DOI: 10.6084/m9.figshare.15145980.v1
title: Additional file 3 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 3 : Table S2. Annotated quantified transcripts for RSEM&gt;10.
DOI: 10.6084/m9.figshare.15145983
title: Additional file 4 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 4 : Table S3. Common cell marker counts.
DOI: 10.6084/m9.figshare.15145986
title: Additional file 5 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 5 : Table S4. SRSF1 transcript counts.
DOI: 10.6084/m9.figshare.15145989
title: Additional file 6 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 6 : Table S5. Differentially-expressed transcripts in patient-derived neurons.
DOI: 10.6084/m9.figshare.15145989.v1
title: Additional file 6 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 6 : Table S5. Differentially-expressed transcripts in patient-derived neurons.
DOI: 10.6084/m9.figshare.15145992.v1
title: Additional file 7 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 7 : Table S6. Gene ontology analysis in patient-derived neurons.
DOI: 10.6084/m9.figshare.15145986.v1
title: Additional file 5 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 5 : Table S4. SRSF1 transcript counts.
DOI: 10.6084/m9.figshare.15145992
title: Additional file 7 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 7 : Table S6. Gene ontology analysis in patient-derived neurons.
DOI: 10.6084/m9.figshare.15145998.v1
title: Additional file 9 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 9 : Table S7. Splicing analysis in patient-derived neurons.
DOI: 10.6084/m9.figshare.15145980
title: Additional file 3 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 3 : Table S2. Annotated quantified transcripts for RSEM&gt;10.
DOI: 10.6084/m9.figshare.15145983.v1
title: Additional file 4 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 4 : Table S3. Common cell marker counts.
DOI: 10.6084/m9.figshare.15145998
title: Additional file 9 of SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis

description: Additional file 9 : Table S7. Splicing analysis in patient-derived neurons.
DOI: 10.6084/m9.figshare.15145479
title: Intensity_map_pl46.txt

description: This is our raw x-ray intensity map for sodium in plagioclase of slide , 46 of 76535.
DOI: 10.6084/m9.figshare.15145479.v1
title: Intensity_map_pl46.txt

description: This is our raw x-ray intensity map for sodium in plagioclase of slide , 46 of 76535.
DOI: 10.6084/m9.figshare.15145482.v1
title: Intensity_map_ol46.txt

description: This is our raw x-ray intensity map for phosphorus in olivine of slide , 46 of 76535.
DOI: 10.6084/m9.figshare.15145482
title: Intensity_map_ol46.txt

description: This is our raw x-ray intensity map for phosphorus in olivine of slide , 46 of 76535.
DOI: 10.6084/m9.figshare.15145485
title: Intensity_map_Pl52.txt

description: This is our raw x-ray intensity map for sodium in plagioclase of slide , 52 of 76535.
DOI: 10.6084/m9.figshare.15145485.v1
title: Intensity_map_Pl52.txt

description: This is our raw x-ray intensity map for sodium in plagioclase of slide , 52 of 76535.
DOI: 10.6084/m9.figshare.15145488.v1
title: Intensity_map_ol52.txt

description: This is our raw x-ray intensity map for phosphorus in olivine of slide , 52 of 76535.
DOI: 10.13140/rg.2.2.23776.81921
title: The complete chloroplast genome of Prunus campanulata ‘double flowers’ (Rosaceae)