cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16667073.v1
title: The landscape of accessible chromatin in quiescent cardiac fibroblasts and cardiac fibroblasts activated after myocardial infarction

description: After myocardial infarction, the massive death of cardiomyocytes leads to cardiac fibroblast proliferation and myofibroblast differentiation, which contributes to the extracellular matrix remodeling of the infarcted myocardium. We recently found that myofibroblasts further differentiate into matrifibrocytes, a newly identified cardiac fibroblast differentiation state. Cardiac fibroblasts of different states have distinct gene expression profiles closely related to their functions. However, the mechanism responsible for the gene expression changes during these activation and differentiation events is still not clear. In this study, the gene expression profiling and genome-wide accessible chromatin mapping of mouse cardiac fibroblasts isolated from the uninjured myocardium and the infarct at multiple time points corresponding to different differentiation states were performed by RNA sequencing (RNA-seq) and the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), respectively. ATAC-seq peaks were highly enriched in the promoter area and the distal area where enhancers are located. A positive correlation was identified between the expression and promoter accessibility for many dynamically expressed genes, even though evidence showed that mechanisms independent of chromatin accessibility may also contribute to the gene expression changes in cardiac fibroblasts after MI. Moreover, motif enrichment analysis and gene regulatory network construction identified transcription factors that possibly contributed to the differential gene expression between cardiac fibroblasts of different states.
DOI: 10.6084/m9.figshare.14569970.v1
title: Additional file 3 of The genetic mechanism of heterosis utilization in maize improvement

description: Additional file 3. Prediction precision of the thirty F1 populations.
DOI: 10.6084/m9.figshare.12997079.v1
title: Additional file 3 of Metabolic and transcriptome responses of RNAi-mediated AMPKα knockdown in Tribolium castaneum

description: Additional file 3.
DOI: 10.6084/m9.figshare.13521147
title: Additional file 4 of Host cell response and distinct gene expression profiles at different stages of Chlamydia trachomatis infection reveals stage-specific biomarkers of infection

description: Additional file 4: Supplementary Table 1 List of Primers used in this study.
DOI: 10.6084/m9.figshare.20861164
title: Additional file 9 of Trem2 deletion enhances tau dispersion and pathology through microglia exosomes

description: Additional file 9: Table S2. DEP analysis from Trem2 KO and WT microglia under steady-state and tau (run 1) or LPS/ATP-treated (run 2) conditions; GO KEGG, BP (Biological Process), CC (Cellular Component), and MF (Molecular Function) analysis using GO DAVID.
DOI: 10.6084/m9.figshare.13520838
title: Additional file 8 of In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants

description: Additional file 8. A detailed list of alternative poly(A) sites with high coverage (more than 1 RT-stop per nucleotide) in deproteinized libraries.
DOI: 10.6084/m9.figshare.13520841.v1
title: Additional file 9 of In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants

description: Additional file 9. The position information of Poly(A) signal motif AAUAAA.
DOI: 10.5281/zenodo.10372618
title: FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Datasets Built on FragPipe

description: Fully processes data using FLiPPR and accompanying python scripts.
description: In the burgeoning field of structural proteomics, the study of protein structure and dynamics across proteomes, limited proteolysis mass spectrometry (LiP-MS) has become a standout approach owing to its ability to offer residue-level insight without requiring specialized equipment. The paper introduces FLiPPR (FragPipe LiP Processor), a novel computational tool designed to enhance the analysis of LiP-MS data by incorporating and building upon the algorithms in FragPipe. FLiPPR addresses the inherent challenges of LiP-MS data analysis by implementing a unique missing data imputation heuristic and introducing both a new data merging approach from ions to cut-sites and a protein-centric multiple hypothesis correction scheme. These methodologies collectively produce datasets that are robust and streamlined. The authors present FLiPPR as a contribution to the standardization of LiP-MS analysis, making it more accessible and systematic for broader application in structural proteomic investigations.The paper details a key improvement of FLiPPR over previous methods: the careful use of missing data to reveal significant structural changes in proteins. This is complemented by a unique merging scheme for ions, peptides, and cut-sites and an innovative multiple hypothesis correction tailored at the protein level. FLiPPR can be seamlessly integrated with FragPipe output, offering robustness and rapid analysis to facilitate future LiP-MS studies. The work also showcases the reanalysis of previous LiP-MS datasets using FLiPPR, leading to sharper statistical trends and underscoring the potential of FLiPPR for LiP-MS data processing.

-- ScienceCast
DOI: 10.5281/zenodo.10372617
title: FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Datasets Built on FragPipe

description: Fully processes data using FLiPPR and accompanying python scripts.
description: In the burgeoning field of structural proteomics, the study of protein structure and dynamics across proteomes, limited proteolysis mass spectrometry (LiP-MS) has become a standout approach owing to its ability to offer residue-level insight without requiring specialized equipment. The paper introduces FLiPPR (FragPipe LiP Processor), a novel computational tool designed to enhance the analysis of LiP-MS data by incorporating and building upon the algorithms in FragPipe. FLiPPR addresses the inherent challenges of LiP-MS data analysis by implementing a unique missing data imputation heuristic and introducing both a new data merging approach from ions to cut-sites and a protein-centric multiple hypothesis correction scheme. These methodologies collectively produce datasets that are robust and streamlined. The authors present FLiPPR as a contribution to the standardization of LiP-MS analysis, making it more accessible and systematic for broader application in structural proteomic investigations.The paper details a key improvement of FLiPPR over previous methods: the careful use of missing data to reveal significant structural changes in proteins. This is complemented by a unique merging scheme for ions, peptides, and cut-sites and an innovative multiple hypothesis correction tailored at the protein level. FLiPPR can be seamlessly integrated with FragPipe output, offering robustness and rapid analysis to facilitate future LiP-MS studies. The work also showcases the reanalysis of previous LiP-MS datasets using FLiPPR, leading to sharper statistical trends and underscoring the potential of FLiPPR for LiP-MS data processing.

-- ScienceCast
DOI: 10.5281/zenodo.10695391
title: FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Datasets Built on FragPipe

description: Fully processes data using FLiPPR and accompanying python scripts.
description: In the burgeoning field of structural proteomics, the study of protein structure and dynamics across proteomes, limited proteolysis mass spectrometry (LiP-MS) has become a standout approach owing to its ability to offer residue-level insight without requiring specialized equipment. The paper introduces FLiPPR (FragPipe LiP Processor), a novel computational tool designed to enhance the analysis of LiP-MS data by incorporating and building upon the algorithms in FragPipe. FLiPPR addresses the inherent challenges of LiP-MS data analysis by implementing a unique missing data imputation heuristic and introducing both a new data merging approach from ions to cut-sites and a protein-centric multiple hypothesis correction scheme. These methodologies collectively produce datasets that are robust and streamlined. The authors present FLiPPR as a contribution to the standardization of LiP-MS analysis, making it more accessible and systematic for broader application in structural proteomic investigations.The paper details a key improvement of FLiPPR over previous methods: the careful use of missing data to reveal significant structural changes in proteins. This is complemented by a unique merging scheme for ions, peptides, and cut-sites and an innovative multiple hypothesis correction tailored at the protein level. FLiPPR can be seamlessly integrated with FragPipe output, offering robustness and rapid analysis to facilitate future LiP-MS studies. The work also showcases the reanalysis of previous LiP-MS datasets using FLiPPR, leading to sharper statistical trends and underscoring the potential of FLiPPR for LiP-MS data processing.

-- ScienceCast
DOI: 10.5281/zenodo.10697466
title: FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Datasets Built on FragPipe

description: Fully processes data using FLiPPR and accompanying python scripts.
description: In the burgeoning field of structural proteomics, the study of protein structure and dynamics across proteomes, limited proteolysis mass spectrometry (LiP-MS) has become a standout approach owing to its ability to offer residue-level insight without requiring specialized equipment. The paper introduces FLiPPR (FragPipe LiP Processor), a novel computational tool designed to enhance the analysis of LiP-MS data by incorporating and building upon the algorithms in FragPipe. FLiPPR addresses the inherent challenges of LiP-MS data analysis by implementing a unique missing data imputation heuristic and introducing both a new data merging approach from ions to cut-sites and a protein-centric multiple hypothesis correction scheme. These methodologies collectively produce datasets that are robust and streamlined. The authors present FLiPPR as a contribution to the standardization of LiP-MS analysis, making it more accessible and systematic for broader application in structural proteomic investigations.The paper details a key improvement of FLiPPR over previous methods: the careful use of missing data to reveal significant structural changes in proteins. This is complemented by a unique merging scheme for ions, peptides, and cut-sites and an innovative multiple hypothesis correction tailored at the protein level. FLiPPR can be seamlessly integrated with FragPipe output, offering robustness and rapid analysis to facilitate future LiP-MS studies. The work also showcases the reanalysis of previous LiP-MS datasets using FLiPPR, leading to sharper statistical trends and underscoring the potential of FLiPPR for LiP-MS data processing.

-- ScienceCast
DOI: 10.6084/m9.figshare.14569979
title: Additional file 6 of The genetic mechanism of heterosis utilization in maize improvement

description: Additional file 6. The merged QTLs and genetic effects detected by the three traits.
DOI: 10.6084/m9.figshare.14569976
title: Additional file 5 of The genetic mechanism of heterosis utilization in maize improvement

description: Additional file 5. QTL summary for three traits detected by GWAS across the maternal and 30 F1 populations.
DOI: 10.6084/m9.figshare.14569979.v1
title: Additional file 6 of The genetic mechanism of heterosis utilization in maize improvement

description: Additional file 6. The merged QTLs and genetic effects detected by the three traits.
DOI: 10.6084/m9.figshare.20336828
title: Additional file 2 of Preoperative chemoradiotherapy with capecitabine and triweekly oxaliplatin versus capecitabine monotherapy for locally advanced rectal cancer: a propensity-score matched study

description: Additional file 2. Original data.
DOI: 10.6084/m9.figshare.14569970
title: Additional file 3 of The genetic mechanism of heterosis utilization in maize improvement

description: Additional file 3. Prediction precision of the thirty F1 populations.
DOI: 10.6084/m9.figshare.13521294
title: Additional file 5 of Histone modifications during the life cycle of the brown alga Ectocarpus

description: Additional file 5: Table S1. Histone proteins in Ectocarpus. Table S4. H4K20me3 peaks associated with different transposon families. Table S5. Genes with significantly different transcript abundances during the gametophyte and sporophyte generations. Table S6. Identification of enriched functional categories in the proteins encoded by the generation-biased gene set. Table S7. The generation-biased gene set is enriched in secreted proteins. Table S8. Analysis of long non-coding RNA genes that were differentially expressed during the gametophyte and sporophyte generations. Table S9. lncRNA GBGs with an adjacent protein-coding GBG. Table S10. Presence and absence of polycomb complex proteins in animals, land plants and stramenopiles. Table S11. Anti-histone-PTM antibodies used in this study. Table S12. Sequence data generated by this study. Table S13. Presence or absence of histone PTMs and RNA-seq TPMs for all Ectocarpus genes in the sporophyte and the gametophyte generations.
DOI: 10.6084/m9.figshare.20336828.v1
title: Additional file 2 of Preoperative chemoradiotherapy with capecitabine and triweekly oxaliplatin versus capecitabine monotherapy for locally advanced rectal cancer: a propensity-score matched study

description: Additional file 2. Original data.
DOI: 10.5281/zenodo.10697416
title: Dataset related to article: DIFFERENT TAU FIBRIL TYPES REDUCE PRION LEVEL IN CHRONICALLY AND DE NOVO INFECTED CELLS

description: Transmission electron microscopy images of Tau fibrils (Figure n. S1 - c)
DOI: 10.5281/zenodo.10697417
title: Dataset related to article: DIFFERENT TAU FIBRIL TYPES REDUCE PRION LEVEL IN CHRONICALLY AND DE NOVO INFECTED CELLS

description: Transmission electron microscopy images of Tau fibrils (Figure n. S1 - c)
DOI: 10.6084/m9.figshare.13521073.v1
title: Additional file 2 of Compacting a synthetic yeast chromosome arm

description: Additional file 2: Table S1. The information of loxPsym fragments in synXIIL.
DOI: 10.15468/dl.7wuaqe
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Romulea longipes Schltr."
 ]
}

 The dataset includes 57 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098435-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/impa-c123-106620
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106359
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106711
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105422
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105641
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106485
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106301
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.15468/dl.53z55d
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhopalopilia hallei Villiers"
 ]
}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098437-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/impa-c123-105618
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106758
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106784
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.15468/dl.hvkyzf
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Fulvius anthocoroides (Reuter, 1875)"
 ]
}

 The dataset includes 36 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098438-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/impa-c123-106671
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106590
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.15468/dl.x975vf
title: Occurrence Download

description: A dataset containing 310 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rubia petiolaris DC."
 ]
}

 The dataset includes 310 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098439-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/impa-c123-105352
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105678
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106644
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.15468/dl.3acwfy
title: Occurrence Download

description: A dataset containing 1222402 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tringa glareola Linnaeus, 1758"
 ]
}

 The dataset includes 1222402 records from 1074 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098423-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/impa-c123-105637
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105963
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.15468/dl.ahmew8
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Romulea lutea J.C.Manning & Goldblatt"
 ]
}

 The dataset includes 7 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098440-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/impa-c123-105746
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105755
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105341
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106465
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105411
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106602
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105689
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.15468/dl.x58jpd
title: Occurrence Download

description: A dataset containing 217 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhopalopilia pallens Pierre"
 ]
}

 The dataset includes 217 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098441-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/impa-c123-106472
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106496
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106457
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106789
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105722
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106190
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105696
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105944
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106177
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.15468/dl.na87g6
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rubia philippinensis Elmer"
 ]
}

 The dataset includes 10 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098442-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/impa-c123-105556
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105620
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106748
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106207
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106508
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.15468/dl.rgzhac
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Romulea luteiflora (M.P.de Vos) M.P.de Vos"
 ]
}

 The dataset includes 68 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098443-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/impa-c123-105738
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106514
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106288
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105829
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.15468/dl.wkprxu
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhopalosciadium stereocalyx Rech.fil."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098444-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/impa-c123-106670
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106217
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105721
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106716
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106783
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106804
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106454
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.15468/dl.fw5mww
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rubia pianmaensis R.Li & H.Li"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098445-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/impa-c123-105997
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106282
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105344
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106698
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-106322
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105765
title: Mission and Diakonia Archives, VID, Stavanger
DOI: 10.25549/impa-c123-105336
title: Mission and Diakonia Archives, VID, Stavanger