cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19311374
title: Additional file 1 of ECNano: A cost-effective workflow for target enrichment sequencing and accurate variant calling on 4800 clinically significant genes using a single MinION flowcell

description: Additional file 1: The performance of Clair-ensemble at target positions using two HG001 sequencing datasets and one HG002 sequencing dataset against the GRCh38 reference genome. The benchmarking results were compared against the original Clair settings with different models, LongShot and Medaka, using ECNano data. LongShot does not provide an INDEL calling function.
DOI: 10.6084/m9.figshare.19311374.v1
title: Additional file 1 of ECNano: A cost-effective workflow for target enrichment sequencing and accurate variant calling on 4800 clinically significant genes using a single MinION flowcell

description: Additional file 1: The performance of Clair-ensemble at target positions using two HG001 sequencing datasets and one HG002 sequencing dataset against the GRCh38 reference genome. The benchmarking results were compared against the original Clair settings with different models, LongShot and Medaka, using ECNano data. LongShot does not provide an INDEL calling function.
DOI: 10.25345/c57m0422d
title: MassIVE Reanalysis RMSV000000355.327 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ST14 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5cc0tv77
title: MassIVE Reanalysis RMSV000000355.322 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RPS14P3 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c53t9d783
title: MassIVE Reanalysis RMSV000000355.331 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, FBXW12 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19311394
title: Additional file 10 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 10: Table S6. Enrichr outputs of MSigDB Hallmark pathways (A, C, E, G) and GO biological processes (B, D, F, H) significantly associated with differentially expressed genes containing differentially methylated promoters and/or gene bodies. A, B Epithelial cell preferred genes with increased average promoter and genebody mCG methylation levels in fiber cells. C, D Fiber cell preferred genes with decreased average promoter and genebody mCG methylation levels in fiber cells. E, F Epithelial cell preferred genes with increased average promoter mCG methylation levels in fiber cells. G, H Fiber cell preferred genes with decreased average promoter mCG methylation levels in fiber cells.
DOI: 10.6084/m9.figshare.19311394.v1
title: Additional file 10 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 10: Table S6. Enrichr outputs of MSigDB Hallmark pathways (A, C, E, G) and GO biological processes (B, D, F, H) significantly associated with differentially expressed genes containing differentially methylated promoters and/or gene bodies. A, B Epithelial cell preferred genes with increased average promoter and genebody mCG methylation levels in fiber cells. C, D Fiber cell preferred genes with decreased average promoter and genebody mCG methylation levels in fiber cells. E, F Epithelial cell preferred genes with increased average promoter mCG methylation levels in fiber cells. G, H Fiber cell preferred genes with decreased average promoter mCG methylation levels in fiber cells.
DOI: 10.6084/m9.figshare.19311397
title: Additional file 11 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 11: Table S7. Differentially methylated mCG regions that are at least partially contained within open chromatin regions.
DOI: 10.6084/m9.figshare.19311397.v1
title: Additional file 11 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 11: Table S7. Differentially methylated mCG regions that are at least partially contained within open chromatin regions.
DOI: 10.6084/m9.figshare.19311400
title: Additional file 12 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 12: Table S8. Differentially methylated mCG regions that are at least partially contained within open chromatin regions at A promoters and genebodies of differentially expressed genes, or B only promoters of differentially expressed genes.
DOI: 10.6084/m9.figshare.19311403
title: Additional file 13 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 13: Table S9. Significantly enriched transcription factor binding motifs found within A hypermethylated mCG regions in promoters or genebodies of epithelial cell preferred genes, or B hypomethylated mCG regions in promoters or genebodies of epithelial cell preferred genes.
DOI: 10.6084/m9.figshare.19311403.v1
title: Additional file 13 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 13: Table S9. Significantly enriched transcription factor binding motifs found within A hypermethylated mCG regions in promoters or genebodies of epithelial cell preferred genes, or B hypomethylated mCG regions in promoters or genebodies of epithelial cell preferred genes.
DOI: 10.6084/m9.figshare.19311406.v1
title: Additional file 14 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 14: Table S10. Target binding sites of enriched transcription factor binding motifs along with corresponding methylation changes and gene expression changes. Target binding sites of enriched transcription factor motifs from demethylated DMRs of Fiber cell genes (A), and from methylated DMRs of Epithelial cell genes (B).
DOI: 10.6084/m9.figshare.19311400.v1
title: Additional file 12 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 12: Table S8. Differentially methylated mCG regions that are at least partially contained within open chromatin regions at A promoters and genebodies of differentially expressed genes, or B only promoters of differentially expressed genes.
DOI: 10.6084/m9.figshare.19311406
title: Additional file 14 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 14: Table S10. Target binding sites of enriched transcription factor binding motifs along with corresponding methylation changes and gene expression changes. Target binding sites of enriched transcription factor motifs from demethylated DMRs of Fiber cell genes (A), and from methylated DMRs of Epithelial cell genes (B).
DOI: 10.6084/m9.figshare.19311409.v1
title: Additional file 15 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 15: Table S11. Genes with established lens functions or associations with cataracts that are differentially expressed and contain differentially methylated regions between lens epithelial and fiber cells.
DOI: 10.6084/m9.figshare.19311412
title: Additional file 16 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 16: Table S12. Pearson correlation analysis comparing gene expression changes and methylation changes within open chromatin regions. The analyses were performed on the following conditions: differentially methylated regions at (1) promoters and genebodies, (2) only promoters, (3) open and closed chromatin, (4) only open chromatin, (5) only open chromatin with significant changes in chromatin accessibility between lens epithelial and fiber cells (ATACseq adj.p-val
DOI: 10.6084/m9.figshare.19311409
title: Additional file 15 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 15: Table S11. Genes with established lens functions or associations with cataracts that are differentially expressed and contain differentially methylated regions between lens epithelial and fiber cells.
DOI: 10.6084/m9.figshare.19311412.v1
title: Additional file 16 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 16: Table S12. Pearson correlation analysis comparing gene expression changes and methylation changes within open chromatin regions. The analyses were performed on the following conditions: differentially methylated regions at (1) promoters and genebodies, (2) only promoters, (3) open and closed chromatin, (4) only open chromatin, (5) only open chromatin with significant changes in chromatin accessibility between lens epithelial and fiber cells (ATACseq adj.p-val
DOI: 10.6084/m9.figshare.19311427
title: Additional file 5 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 5: Table S1. Proportion of methylated cytosines that are mCG, mCHG, mCHH in each sample of lens epithelial and fiber cells.
DOI: 10.6084/m9.figshare.19311433
title: Additional file 6 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 6: Table S2. Differentially methylated mCG regions between lens epithelial and fiber cells.
DOI: 10.6084/m9.figshare.19311427.v1
title: Additional file 5 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 5: Table S1. Proportion of methylated cytosines that are mCG, mCHG, mCHH in each sample of lens epithelial and fiber cells.
DOI: 10.6084/m9.figshare.19311433.v1
title: Additional file 6 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 6: Table S2. Differentially methylated mCG regions between lens epithelial and fiber cells.
DOI: 10.6084/m9.figshare.19311436
title: Additional file 7 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 7: Table S3. Differentially expressed genes between lens epithelial cells and fiber cells. A Epithelial preferred genes (FPKM log2FC 0.4, q
DOI: 10.6084/m9.figshare.19311439
title: Additional file 8 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 8: Table S4. Enrichr outputs of GO Biological processes (A, C) and MSigDB Hallmark pathways (B, D) significantly associated with the differentially expressed genes between lens epithelial cells and fiber cells. A, B Top 200 epithelial cell preferred genes, C, D top 200 fiber cell preferred genes.
DOI: 10.6084/m9.figshare.19311442
title: Additional file 9 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 9: Table S5. Average change in mCG methylation level for all differentially methylated mCG regions mapped to A–D the promoters and genebodies of differentially expressed genes, or E–H only the promoters of differentially expressed genes. A, E Epithelial cell preferred genes with increased mCG methylation. B, F Fiber cell preferred genes with decreased mCG methylation. C, G Epithelial cell preferred genes with decreased mCG methylation. D, H Fiber cell preferred genes with increased mCG methylation.
DOI: 10.6084/m9.figshare.19311436.v1
title: Additional file 7 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 7: Table S3. Differentially expressed genes between lens epithelial cells and fiber cells. A Epithelial preferred genes (FPKM log2FC 0.4, q
DOI: 10.6084/m9.figshare.19311439.v1
title: Additional file 8 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 8: Table S4. Enrichr outputs of GO Biological processes (A, C) and MSigDB Hallmark pathways (B, D) significantly associated with the differentially expressed genes between lens epithelial cells and fiber cells. A, B Top 200 epithelial cell preferred genes, C, D top 200 fiber cell preferred genes.
DOI: 10.6084/m9.figshare.19311442.v1
title: Additional file 9 of Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

description: Additional file 9: Table S5. Average change in mCG methylation level for all differentially methylated mCG regions mapped to A–D the promoters and genebodies of differentially expressed genes, or E–H only the promoters of differentially expressed genes. A, E Epithelial cell preferred genes with increased mCG methylation. B, F Fiber cell preferred genes with decreased mCG methylation. C, G Epithelial cell preferred genes with decreased mCG methylation. D, H Fiber cell preferred genes with increased mCG methylation.
DOI: 10.25345/c5028pf5r
title: MassIVE Reanalysis RMSV000000355.333 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, KRT222 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5v97zt0c
title: MassIVE Reanalysis RMSV000000355.335 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, NOP56 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qj7806d
title: MassIVE Reanalysis RMSV000000355.330 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C9orf100 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19311491
title: Additional file 2 of Comparison of total immunoglobulin G antibody responses to different protein fragments of Plasmodium vivax Reticulocyte binding protein 2b

description: Additional file 2. Supplementary data supporting results. Sheet 1. Relative Antibody Units (RAU) for individuals in the 12-month longitudinal cohort conducted in Thailand. Sheet 2. Relative Antibody Units (RAU) for individuals in the symptomatic cohort at time of infection and one-week post infection. Sheet 3. Relative Antibody Units (RAU) for individuals in the three negative control cohorts.
DOI: 10.6084/m9.figshare.19311491.v1
title: Additional file 2 of Comparison of total immunoglobulin G antibody responses to different protein fragments of Plasmodium vivax Reticulocyte binding protein 2b

description: Additional file 2. Supplementary data supporting results. Sheet 1. Relative Antibody Units (RAU) for individuals in the 12-month longitudinal cohort conducted in Thailand. Sheet 2. Relative Antibody Units (RAU) for individuals in the symptomatic cohort at time of infection and one-week post infection. Sheet 3. Relative Antibody Units (RAU) for individuals in the three negative control cohorts.
DOI: 10.25345/c5kw57k62
title: MassIVE Reanalysis RMSV000000355.334 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PWP2 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5g44hs27
title: MassIVE Reanalysis RMSV000000355.328 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, OR5K1 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5bc3sz70
title: MassIVE Reanalysis RMSV000000355.329 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ZNF69 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c56m3353n
title: MassIVE Reanalysis RMSV000000355.337 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SLC22A10 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19311532
title: Additional file 1 of Beating the heat: ecology of desert bobcats

description: Additional file 1: Table S1. Occupancy model results from camera traps. Table S2. BLAST # constructed from biom file.
DOI: 10.6084/m9.figshare.19311532.v1
title: Additional file 1 of Beating the heat: ecology of desert bobcats

description: Additional file 1: Table S1. Occupancy model results from camera traps. Table S2. BLAST # constructed from biom file.
DOI: 10.6084/m9.figshare.19311535.v1
title: Additional file 2 of Beating the heat: ecology of desert bobcats

description: Additional file 2. DNA extraction modifications from Qiagen Qiaamp DNA Stool mini Kit instructions.Modifications listed by corresponding step from Qiagen instructions, un-listed steps remain unchanged.
DOI: 10.6084/m9.figshare.19311538
title: Additional file 3 of Beating the heat: ecology of desert bobcats

description: Additional file 3: Additional Data. All raw data and details from camera trap models are available as Additional file 3.
DOI: 10.6084/m9.figshare.19311535
title: Additional file 2 of Beating the heat: ecology of desert bobcats

description: Additional file 2. DNA extraction modifications from Qiagen Qiaamp DNA Stool mini Kit instructions.Modifications listed by corresponding step from Qiagen instructions, un-listed steps remain unchanged.
DOI: 10.6084/m9.figshare.19311538.v1
title: Additional file 3 of Beating the heat: ecology of desert bobcats

description: Additional file 3: Additional Data. All raw data and details from camera trap models are available as Additional file 3.
DOI: 10.6084/m9.figshare.19311554
title: Additional file 10 of High-throughput sequencing data revealed genotype-specific changes evoked by heat stress in crown tissue of barley sdw1 near-isogenic lines

description: Additional file 10: Table S9. Phenotypic and physiological traits, with analysis.