cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24993805
title: Additional file 2 of RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9

description: Additional file 2: Table S1. Positive regulators of HOXA9 from genome-wide CRISPR/Cas9 screen in OCIAML2 and SEM cells.
DOI: 10.6084/m9.figshare.24993805.v1
title: Additional file 2 of RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9

description: Additional file 2: Table S1. Positive regulators of HOXA9 from genome-wide CRISPR/Cas9 screen in OCIAML2 and SEM cells.
DOI: 10.6084/m9.figshare.26666923
title: Additional file 3 of RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9

description: Additional file 3: Table S2. The differentially expressed genes (DEGs) in RBM5 high group vs. RBM5 low groups from public RNA-seq dataset for 44 AML patients.
DOI: 10.6084/m9.figshare.26666923.v1
title: Additional file 3 of RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9

description: Additional file 3: Table S2. The differentially expressed genes (DEGs) in RBM5 high group vs. RBM5 low groups from public RNA-seq dataset for 44 AML patients.
DOI: 10.6084/m9.figshare.26666926.v1
title: Additional file 4 of RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9

description: Additional file 4: Table S3. RBM5 domain CRISPR/Cas9 screen after 7 days expansion in OCIAML2 cells.
DOI: 10.6084/m9.figshare.26666926
title: Additional file 4 of RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9

description: Additional file 4: Table S3. RBM5 domain CRISPR/Cas9 screen after 7 days expansion in OCIAML2 cells.
DOI: 10.6084/m9.figshare.26666929
title: Additional file 5 of RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9

description: Additional file 5: Table S4. The DEGs in RBM5 KO relative to control and RBM5 OE relative to control.
DOI: 10.6084/m9.figshare.26666929.v1
title: Additional file 5 of RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9

description: Additional file 5: Table S4. The DEGs in RBM5 KO relative to control and RBM5 OE relative to control.
DOI: 10.6084/m9.figshare.26666932
title: Additional file 6 of RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9

description: Additional file 6: Table S5. The associated genes with differential splicing events in RBM5KO and RBM5 OE relative to control.
DOI: 10.6084/m9.figshare.26666932.v1
title: Additional file 6 of RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9

description: Additional file 6: Table S5. The associated genes with differential splicing events in RBM5KO and RBM5 OE relative to control.
DOI: 10.6084/m9.figshare.26666935
title: Additional file 7 of RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9

description: Additional file 7: Table S6. The DEGs in in RBM5 KO cells with HOXA9 overexpression relative to RBM5 KO control.
DOI: 10.6084/m9.figshare.26666935.v1
title: Additional file 7 of RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9

description: Additional file 7: Table S6. The DEGs in in RBM5 KO cells with HOXA9 overexpression relative to RBM5 KO control.
DOI: 10.6084/m9.figshare.26666938
title: Additional file 8 of RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9

description: Additional file 8: Table S7. Oligonucleotides, knock-in fragment, primers, and antibodies used in this study.
DOI: 10.6084/m9.figshare.26666938.v1
title: Additional file 8 of RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9

description: Additional file 8: Table S7. Oligonucleotides, knock-in fragment, primers, and antibodies used in this study.
DOI: 10.6084/m9.figshare.24993682
title: Additional file 1 of Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

description: Additional file 1: Table S1. Ligand-receptor pairs between CD8T cells and tumor cells found by niche-LR in the CosMx NSCLC data. Table S2. Ligand-receptor pairs between CD8T cells and tumor cells found via permutation test in the CosMx NSCLC data.
DOI: 10.6084/m9.figshare.24993682.v1
title: Additional file 1 of Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

description: Additional file 1: Table S1. Ligand-receptor pairs between CD8T cells and tumor cells found by niche-LR in the CosMx NSCLC data. Table S2. Ligand-receptor pairs between CD8T cells and tumor cells found via permutation test in the CosMx NSCLC data.
DOI: 10.6084/m9.figshare.24993806
title: Additional file 2 of Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

description: Additional file 2: Table S1. Description of data quality for liver metastasis 10X Visium data.
DOI: 10.6084/m9.figshare.24993806.v1
title: Additional file 2 of Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

description: Additional file 2: Table S1. Description of data quality for liver metastasis 10X Visium data.
DOI: 10.6084/m9.figshare.26666950
title: Additional file 4 of Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

description: Additional file 4: Table S1. A list of (fibroblast, tumor)+ genes found by niche-DE in the integrated 10X liver metastasis colorectal cancer data. Table S2. The list of enriched pathways found by enrichR using the gene list in table S1. Table S3. The list of ligand-receptor pairs found by niche-LR for fibroblasts near tumor cells.
DOI: 10.6084/m9.figshare.26666950.v1
title: Additional file 4 of Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

description: Additional file 4: Table S1. A list of (fibroblast, tumor)+ genes found by niche-DE in the integrated 10X liver metastasis colorectal cancer data. Table S2. The list of enriched pathways found by enrichR using the gene list in table S1. Table S3. The list of ligand-receptor pairs found by niche-LR for fibroblasts near tumor cells.
DOI: 10.6084/m9.figshare.26666953
title: Additional file 5 of Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

description: Additional file 5: Table S1. A list of (tumor, fibroblast)- genes found by applying niche-DE only in patient 4 of the manuscript. Table S2. The CODEX protein panel used to generate the CODEX data for patient 4 in the manuscript.
DOI: 10.6084/m9.figshare.26666959
title: Additional file 7 of Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

description: Additional file 7: Table S1. A list of gene markers for fibroblasts when near tumor subclone 1 as opposed to tumor subclone 2 as found by niche-DE. Table S2. A list of gene markers for fibroblasts when near tumor subclone 2 as opposed to tumor subclone 1 as found by niche-DE. Table S3. The list of enriched pathways found by enrichR using the gene list in table S1. Table S4. The list of enriched pathways found by enrichR using the gene list in table S2.
DOI: 10.6084/m9.figshare.26666959.v1
title: Additional file 7 of Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

description: Additional file 7: Table S1. A list of gene markers for fibroblasts when near tumor subclone 1 as opposed to tumor subclone 2 as found by niche-DE. Table S2. A list of gene markers for fibroblasts when near tumor subclone 2 as opposed to tumor subclone 1 as found by niche-DE. Table S3. The list of enriched pathways found by enrichR using the gene list in table S1. Table S4. The list of enriched pathways found by enrichR using the gene list in table S2.
DOI: 10.6084/m9.figshare.26666965
title: Additional file 9 of Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

description: Additional file 9: Table S1. A list of gene markers for macrophages when near tumor cells as opposed to hepatocytes as found by niche-DE. Table S2. A list of gene markers for macrophages when hepatocytes as opposed to tumor cells as found by niche-DE. Table S3. A list of ligand-receptor pairs found by niche-LR for macrophages when near tumor cells. Table S4. A list of (macrophage, tumor)+ genes found by niche-DE in the integrated 10X liver metastasis colorectal cancer data. Table S5. The list of enriched pathways found by enrichR using the gene list in table S4. Table S6. The list of enriched pathways found by enrichR using the gene list in table S1.
DOI: 10.6084/m9.figshare.26666965.v1
title: Additional file 9 of Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

description: Additional file 9: Table S1. A list of gene markers for macrophages when near tumor cells as opposed to hepatocytes as found by niche-DE. Table S2. A list of gene markers for macrophages when hepatocytes as opposed to tumor cells as found by niche-DE. Table S3. A list of ligand-receptor pairs found by niche-LR for macrophages when near tumor cells. Table S4. A list of (macrophage, tumor)+ genes found by niche-DE in the integrated 10X liver metastasis colorectal cancer data. Table S5. The list of enriched pathways found by enrichR using the gene list in table S4. Table S6. The list of enriched pathways found by enrichR using the gene list in table S1.
DOI: 10.6084/m9.figshare.26666968
title: Additional file 10 of Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

description: Additional file 10: Table S1. (Fibroblast, Proximal Tubular)+ cells as found by niche-DE in the integrated 10X Visium fibrotic kidney data. Table S2. Ligand-receptor pairs between fibroblasts and proximal tubular cells found by niche-LR in the integrated 10X Visium fibrotic kidney data. Table S3. The list of enriched pathways found by enrichR using the gene list in table S1. Table S4. (Proximal Tubular, Fibroblast)+ cells as found by niche-DE in the integrated 10X Visium fibrotic kidney data.
DOI: 10.6084/m9.figshare.26666968.v1
title: Additional file 10 of Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

description: Additional file 10: Table S1. (Fibroblast, Proximal Tubular)+ cells as found by niche-DE in the integrated 10X Visium fibrotic kidney data. Table S2. Ligand-receptor pairs between fibroblasts and proximal tubular cells found by niche-LR in the integrated 10X Visium fibrotic kidney data. Table S3. The list of enriched pathways found by enrichR using the gene list in table S1. Table S4. (Proximal Tubular, Fibroblast)+ cells as found by niche-DE in the integrated 10X Visium fibrotic kidney data.
DOI: 10.6084/m9.figshare.24993735
title: Additional file 1 of Evolutionary history of the cytochrome P450s from Colletotrichum species and prediction of their putative functional roles during host-pathogen interactions

description: Additional file 1: Table S1. Number of P450 cytochromes harbored in representative species belonging to Colletotrichum genus.
DOI: 10.15156/bio/sh0199487.10fu
title: SH0199487.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0199488.10fu
title: SH0199488.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0199489.10fu
title: SH0199489.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0199490.10fu
title: SH0199490.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0199491.10fu
title: SH0199491.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0199492.10fu
title: SH0199492.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0199493.10fu
title: SH0199493.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0199494.10fu
title: SH0199494.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0199495.10fu
title: SH0199495.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0199496.10fu
title: SH0199496.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.