cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7386347.v1
title: Additional file 10: of Transcriptome analysis reveals a composite molecular map linked to unique seed oil profile of Neocinnamomum caudatum (Nees) Merr

description: Identification of unigene that involved in lipid metabolisms by Local Blast. Based on the local-blast search against the database with 81 key Arabidopsis genes that are involved in FA formation and triacylglycerol synthesis, we identified 137 unigenes that have high sequence similarities (E-value &lt; 1.0E 10-5) to the Arabidopsis homologs. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.7386419
title: Additional file 13: of Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition

description: Table S11. The detailed information of ribosome acetylated proteins involved in 3hN/0â N Interaction network. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7386419.v1
title: Additional file 13: of Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition

description: Table S11. The detailed information of ribosome acetylated proteins involved in 3hN/0â N Interaction network. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.21542226
title: Additional file 5 of Integrated next-generation sequencing and comparative transcriptomic analysis of leaves provides novel insights into the ethylene pathway of Chrysanthemum morifolium in response to a Chinese isolate of chrysanthemum virus B

description: Additional file 5: Table S4. Summary of RNA sequencing of leaves of Chrysanthemum morifolium, uninfected (healthy) or infected with the Chinese isolate of chrysanthemum virus B (CVB-CN).
DOI: 10.5281/zenodo.8349310
title: Dataset from "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (CD28-mEos3.2)

description: This dataset contains raw microscopy data from the article "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (doi.org/10.1002/anie.202307555)

Zip file contains PALM measurements of HEK293 cells expressing CD28 fused with mEos3.2.Each folder in .zip file contains one PALM measurement (TIFF format) and recording settings (.xml) automatically created by acquiring software. For technical reasons, single measurements are divided into TIFF files of =<4088 frames.

Detailed protocols for sample preparation and data acquisition are described in the article.Some details are listed below.

SAMPLE PREPARATION

cell line: Flp-In™ T-REx™ 293transfection method: modified calcium-phosphate transient transfection [1]fixation method: 4% paraformaldehyde solution in PBS for 30 min at room temperatureimaging buffer: PBS

PALM ACQUISITION

A custom-built setup for single-molecule localization microscopy is described in [2].mEos3.2 was simultaneously photoconverted, imaged and photobleached by gradually increasing UV illumination (405 nm; up to 1 mW at the sample) and continuous excitation at 561 nm (approximately 50 mW at the sample).PALM movies of cell plasma membrane were recorded in total internal reflection fluorescence (TIRF) mode using an EMCCD camera:exposure time = 100 msframe size = 512x512 pixelspixel size = 80 nm

 



Chen C, Okayama H. High-efficiency transformation of mammalian cells by plasmid DNA. Molecular and cellular biology. 1987 Aug 1;7(8):2745-52.

Tang Y, Dai L, Zhang X, Li J, Hendriks J, Fan X, Gruteser N, Meisenberg A, Baumann A, Katranidis A, Gensch T. SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy. Scientific reports. 2015 Jun 22;5(1):11073
DOI: 10.5281/zenodo.8349311
title: Dataset from "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (CD28-mEos3.2)

description: This dataset contains raw microscopy data from the article "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (doi.org/10.1002/anie.202307555)

Zip file contains PALM measurements of HEK293 cells expressing CD28 fused with mEos3.2.Each folder in .zip file contains one PALM measurement (TIFF format) and recording settings (.xml) automatically created by acquiring software. For technical reasons, single measurements are divided into TIFF files of =<4088 frames.

Detailed protocols for sample preparation and data acquisition are described in the article.Some details are listed below.

SAMPLE PREPARATION

cell line: Flp-In™ T-REx™ 293transfection method: modified calcium-phosphate transient transfection [1]fixation method: 4% paraformaldehyde solution in PBS for 30 min at room temperatureimaging buffer: PBS

PALM ACQUISITION

A custom-built setup for single-molecule localization microscopy is described in [2].mEos3.2 was simultaneously photoconverted, imaged and photobleached by gradually increasing UV illumination (405 nm; up to 1 mW at the sample) and continuous excitation at 561 nm (approximately 50 mW at the sample).PALM movies of cell plasma membrane were recorded in total internal reflection fluorescence (TIRF) mode using an EMCCD camera:exposure time = 100 msframe size = 512x512 pixelspixel size = 80 nm

 



Chen C, Okayama H. High-efficiency transformation of mammalian cells by plasmid DNA. Molecular and cellular biology. 1987 Aug 1;7(8):2745-52.

Tang Y, Dai L, Zhang X, Li J, Hendriks J, Fan X, Gruteser N, Meisenberg A, Baumann A, Katranidis A, Gensch T. SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy. Scientific reports. 2015 Jun 22;5(1):11073
DOI: 10.6084/m9.figshare.21542232
title: Additional file 7 of Integrated next-generation sequencing and comparative transcriptomic analysis of leaves provides novel insights into the ethylene pathway of Chrysanthemum morifolium in response to a Chinese isolate of chrysanthemum virus B

description: Additional file 7: Table S6. Significant differentially expressed genes (SDEGs) identified in leaves of Chrysanthemum morifolium during infection with the Chinese isolate of chrysanthemum virus B (CVB-CN).
DOI: 10.6084/m9.figshare.7386488.v1
title: Additional file 18: of Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition

description: Table S16. The detailed information of ribosome acetylated proteins involved in 3dN/3hN Interaction network. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7386431
title: Additional file 14: of Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition

description: Table S12. The detailed information of proteins involved in 3dN/0â N Interaction network. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.21542238.v1
title: Additional file 9 of Integrated next-generation sequencing and comparative transcriptomic analysis of leaves provides novel insights into the ethylene pathway of Chrysanthemum morifolium in response to a Chinese isolate of chrysanthemum virus B

description: Additional file 9: Table S8. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the significant differentially expressed genes (SDEGs) of Chrysanthemum morifolium responding to infection with the Chinese isolate of chrysanthemum virus B (CVB-CN).
DOI: 10.6084/m9.figshare.7386497
title: Additional file 7: of Transcriptome analysis reveals a composite molecular map linked to unique seed oil profile of Neocinnamomum caudatum (Nees) Merr

description: Functional annotations of unigenes in N. caudatum developing seeds. (XLSX 15909 kb)
DOI: 10.6084/m9.figshare.7386497.v1
title: Additional file 7: of Transcriptome analysis reveals a composite molecular map linked to unique seed oil profile of Neocinnamomum caudatum (Nees) Merr

description: Functional annotations of unigenes in N. caudatum developing seeds. (XLSX 15909 kb)
DOI: 10.6084/m9.figshare.19445138
title: Additional file 3 of Prognostic significance of SNCA and its methylation in bladder cancer

description: Additional file 3.
DOI: 10.6084/m9.figshare.19445141
title: Additional file 4 of Prognostic significance of SNCA and its methylation in bladder cancer

description: Additional file 4.
DOI: 10.6084/m9.figshare.21542211
title: Additional file 12 of Integrated next-generation sequencing and comparative transcriptomic analysis of leaves provides novel insights into the ethylene pathway of Chrysanthemum morifolium in response to a Chinese isolate of chrysanthemum virus B

description: Additional file 12: Table S11. Significant differentially expressed genes (SDEGs) in Chrysanthemum morifolium following infection with the Chinese isolate of chrysanthemum virus B (CVB-CN) implicated in the ethylene pathway established according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and previous studies on the model plant species Arabidopsis.
DOI: 10.6084/m9.figshare.19445150.v1
title: Additional file 7 of Prognostic significance of SNCA and its methylation in bladder cancer

description: Additional file 7.
DOI: 10.6084/m9.figshare.7386518.v1
title: Additional file 9: of Transcriptome analysis reveals a composite molecular map linked to unique seed oil profile of Neocinnamomum caudatum (Nees) Merr

description: KEGG annotation of DEGs in the developing seeds of N. caudatum. KEGG annotations of DEGs among three contrast groups were performed with KASS). (XLSX 133 kb)
DOI: 10.6084/m9.figshare.19445135.v1
title: Additional file 2 of Prognostic significance of SNCA and its methylation in bladder cancer

description: Additional file 2.
DOI: 10.6084/m9.figshare.19445138.v1
title: Additional file 3 of Prognostic significance of SNCA and its methylation in bladder cancer

description: Additional file 3.
DOI: 10.6084/m9.figshare.7386518
title: Additional file 9: of Transcriptome analysis reveals a composite molecular map linked to unique seed oil profile of Neocinnamomum caudatum (Nees) Merr

description: KEGG annotation of DEGs in the developing seeds of N. caudatum. KEGG annotations of DEGs among three contrast groups were performed with KASS). (XLSX 133 kb)
DOI: 10.6084/m9.figshare.19445144
title: Additional file 5 of Prognostic significance of SNCA and its methylation in bladder cancer

description: Additional file 5.
DOI: 10.6084/m9.figshare.19445147.v1
title: Additional file 6 of Prognostic significance of SNCA and its methylation in bladder cancer

description: Additional file 6.
DOI: 10.6084/m9.figshare.19445150
title: Additional file 7 of Prognostic significance of SNCA and its methylation in bladder cancer

description: Additional file 7.
DOI: 10.6084/m9.figshare.21542205
title: Additional file 10 of Integrated next-generation sequencing and comparative transcriptomic analysis of leaves provides novel insights into the ethylene pathway of Chrysanthemum morifolium in response to a Chinese isolate of chrysanthemum virus B

description: Additional file 10: Table S9. Significant differentially expressed genes (SDEGs) in leaves of Chrysanthemum morifolium implicated in transcription and transcription regulation during infection with the Chinese isolate of chrysanthemum virus B (CVB-CN).
DOI: 10.6084/m9.figshare.7386464.v1
title: Additional file 16: of Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition

description: Table S14. The detailed information of ribosome acetylated proteins involved in 3dN/0â N Interaction network. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.21542208
title: Additional file 11 of Integrated next-generation sequencing and comparative transcriptomic analysis of leaves provides novel insights into the ethylene pathway of Chrysanthemum morifolium in response to a Chinese isolate of chrysanthemum virus B

description: Additional file 11: Table S10. Significant differentially expressed genes (SDEGs) in leaves of Chrysanthemum morifolium involved in ethylene pathway based on gene ontology (GO) analysis during infection with the Chinese isolate of chrysanthemum virus B (CVB-CN).
DOI: 10.6084/m9.figshare.7386512
title: Additional file 1: of Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition

description: Table S1. The detailed information for reagents used in the study. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7386512.v1
title: Additional file 1: of Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition

description: Table S1. The detailed information for reagents used in the study. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.12629419
title: Additional file 4 of Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing

description: Additional File 4. DEGs expression under the heat stress of pearl millet
DOI: 10.6084/m9.figshare.7386551.v1
title: Additional file 5: of Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition

description: Table S4. The numbers of identified modification sites per protein (XLSX 35 kb)
DOI: 10.35003/yspchc/gqw1n1
title: fig2.pptx

description: :unav
DOI: 10.6084/m9.figshare.19445147
title: Additional file 6 of Prognostic significance of SNCA and its methylation in bladder cancer

description: Additional file 6.
DOI: 10.35003/yspchc/hkel4w
title: fig1.pptx

description: :unav
DOI: 10.6084/m9.figshare.19445141.v1
title: Additional file 4 of Prognostic significance of SNCA and its methylation in bladder cancer

description: Additional file 4.
DOI: 10.6084/m9.figshare.12629422.v1
title: Additional file 5 of Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing

description: Additional File 5. DEGs expression under the drought stress of pearl millet
DOI: 10.6084/m9.figshare.21542220
title: Additional file 3 of Integrated next-generation sequencing and comparative transcriptomic analysis of leaves provides novel insights into the ethylene pathway of Chrysanthemum morifolium in response to a Chinese isolate of chrysanthemum virus B

description: Additional file 3: Table S2. Contigs mapped in the viral genome of the Chinese isolate of chrysanthemum virus B (CVB-CN).
DOI: 10.35003/yspchc/vbenik
title: fig5.pptx

description: :unav
DOI: 10.6084/m9.figshare.12629413.v1
title: Additional file 2 of Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing

description: Additional file 2. Photosynthesis-related gene expression under heat stress
DOI: 10.6084/m9.figshare.12629416
title: Additional file 3 of Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing

description: Additional file 3. Expression of Glycerophospholipid metabolic related genes during drought stress
DOI: 10.6084/m9.figshare.12629416.v1
title: Additional file 3 of Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing

description: Additional file 3. Expression of Glycerophospholipid metabolic related genes during drought stress
DOI: 10.6084/m9.figshare.12629422
title: Additional file 5 of Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing

description: Additional File 5. DEGs expression under the drought stress of pearl millet
DOI: 10.6084/m9.figshare.7386530.v1
title: Additional file 3: of Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition

description: Table S2. The Chlorophyll fluorescence parameter (Fv/Fm) and N contents. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.12629419.v1
title: Additional file 4 of Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing

description: Additional File 4. DEGs expression under the heat stress of pearl millet
DOI: 10.6084/m9.figshare.21542232.v1
title: Additional file 7 of Integrated next-generation sequencing and comparative transcriptomic analysis of leaves provides novel insights into the ethylene pathway of Chrysanthemum morifolium in response to a Chinese isolate of chrysanthemum virus B

description: Additional file 7: Table S6. Significant differentially expressed genes (SDEGs) identified in leaves of Chrysanthemum morifolium during infection with the Chinese isolate of chrysanthemum virus B (CVB-CN).
DOI: 10.6084/m9.figshare.21542235
title: Additional file 8 of Integrated next-generation sequencing and comparative transcriptomic analysis of leaves provides novel insights into the ethylene pathway of Chrysanthemum morifolium in response to a Chinese isolate of chrysanthemum virus B

description: Additional file 8: Table S7. Gene ontology (GO) enrichment analysis of the significant differentially expressed genes (SDEGs) of Chrysanthemum morifolium responding to infection with the Chinese isolate of chrysanthemum virus B (CVB-CN).
DOI: 10.6084/m9.figshare.21542235.v1
title: Additional file 8 of Integrated next-generation sequencing and comparative transcriptomic analysis of leaves provides novel insights into the ethylene pathway of Chrysanthemum morifolium in response to a Chinese isolate of chrysanthemum virus B

description: Additional file 8: Table S7. Gene ontology (GO) enrichment analysis of the significant differentially expressed genes (SDEGs) of Chrysanthemum morifolium responding to infection with the Chinese isolate of chrysanthemum virus B (CVB-CN).
DOI: 10.35003/yspchc/rc0bdj
title: Mappe1.tab

description: :unav
DOI: 10.6084/m9.figshare.21542068.v1
title: Additional file 7 of MAPK8IP2 is a potential prognostic biomarker and promote tumor progression in prostate cancer

description: Additional file 7 Table S2. Gene Ontology term enrichment analysis of the MAPK8IP2 gene and its partner genes.
DOI: 10.6084/m9.figshare.7386476
title: Additional file 17: of Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition

description: Table S15. The detailed information of proteins involved in 3dN/3hN Interaction network. (XLSX 23 kb)
DOI: 10.5281/zenodo.10624824
title: Data for "Tuning Structural and Electronic Properties of Metal-Organic Framework 5 by Metal Substitution and Linker Functionalization"

description: The AiiDA archives of the high-throughput calculations presented in the paper “Tuning Structural and Electronic Properties of Metal-Organic Framework 5 by Metal Substitution and Linker Functionalization”

The files “*_MOF_workflows.aiida” contains the actual calculation data for metal nodes Be, Ba, Ca, Cd, Mg, Sr, and Zn and the files with suffix “*.yaml” contain configuration files of the workflows. Additional data on the elemental phases can be retrieved https://zenodo.org/records/10082633.
DOI: 10.5281/zenodo.10624825
title: Data for "Tuning Structural and Electronic Properties of Metal-Organic Framework 5 by Metal Substitution and Linker Functionalization"

description: The AiiDA archives of the high-throughput calculations presented in the paper “Tuning Structural and Electronic Properties of Metal-Organic Framework 5 by Metal Substitution and Linker Functionalization”

The files “*_MOF_workflows.aiida” contains the actual calculation data for metal nodes Be, Ba, Ca, Cd, Mg, Sr, and Zn and the files with suffix “*.yaml” contain configuration files of the workflows. Additional data on the elemental phases can be retrieved https://zenodo.org/records/10082633.
DOI: 10.6084/m9.figshare.7386539.v1
title: Additional file 1: of GRIPT: a novel case-control analysis method for Mendelian disease gene discovery

description: Table S1. The sensitivity and specificity of GRIPT with CADD and other tests under the AR and AD models. Table S2. Benchmark on 400 randomly selected known disease genes. Table S3. Test the effect of the patient cohort sample size. Table S4. Test the effect of population stratification in cohorts. Table S5. Test the effect of variant frequency filtering. Table S6. Test the effect of the control cohort size. Table S7. The performance of detecting genes with modest-effect variants. (XLSX 111Â kb)
DOI: 10.6084/m9.figshare.18393149
title: Additional file 7 of Assembly and comparative analysis of the first complete mitochondrial genome of Acer truncatum Bunge: a woody oil-tree species producing nervonic acid

description: Additional file 7: Table S3. The repeat sequences distributions in the A. yangbiense mitogenome genome.
DOI: 10.6084/m9.figshare.7386488
title: Additional file 18: of Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition

description: Table S16. The detailed information of ribosome acetylated proteins involved in 3dN/3hN Interaction network. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.12629461
title: Additional file 4 of Integrated assessment of biomarker responses and comparative toxicity pathway in snails Bellamya aeruginosa exposed to tributyltin and triphenyltin in sediments

description: Additional file 4. The annotation of DEGs between the control group and triphenyltin treatment group.
DOI: 10.6084/m9.figshare.21542268.v1
title: Additional file 2 of The predictive effect of direct-indirect bilirubin ratio on clinical events in acute coronary syndrome: results from an observational cohort study in north China

description: Supplementary Material 2: Z test of AUCs in Figure 2
DOI: 10.6084/m9.figshare.7386500.v1
title: Additional file 19: of Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition

description: Table S17. The detailed information of photosynthesis acetylated proteins involved in 3dN/3hN Interaction network. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.12629452
title: Additional file 1 of Integrated assessment of biomarker responses and comparative toxicity pathway in snails Bellamya aeruginosa exposed to tributyltin and triphenyltin in sediments

description: Additional file 1. The annotation of DEGs between the tributyltin treatment group and the control group.
DOI: 10.6084/m9.figshare.7386581.v1
title: Additional file 7: of Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition

description: Table S5. Peptide motif. (XLSX 485 kb)
DOI: 10.5281/zenodo.8349352
title: Dataset from "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (wtChR2-mEos3.2)

description: This dataset contains raw microscopy data from the article "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (doi.org/10.1002/anie.202307555)

Zip file contains PALM measurements of HEK293 cells expressing ChR2WT fused with mEos3.2.Each folder in .zip file contains one PALM measurement (TIFF format) and recording settings (.xml) automatically created by acquiring software. For technical reasons, single measurements are divided into TIFF files of =<4088 frames.

Detailed protocols for sample preparation and data acquisition are described in the article.Some details are listed below.

SAMPLE PREPARATION

cell line: Flp-In™ T-REx™ 293transfection method: modified calcium-phosphate transient transfection [1]fixation method: 4% paraformaldehyde solution in PBS for 30 min at room temperatureimaging buffer: PBS

PALM ACQUISITION

A custom-built setup for single-molecule localization microscopy is described in [2].mEos3.2 was simultaneously photoconverted, imaged and photobleached by gradually increasing UV illumination (405 nm; up to 1 mW at the sample) and continuous excitation at 561 nm (approximately 50 mW at the sample).PALM movies of cell plasma membrane were recorded in total internal reflection fluorescence (TIRF) mode using an EMCCD camera:exposure time = 100 msframe size = 512x512 pixelspixel size = 80 nm

 

[1] Chen C, Okayama H. High-efficiency transformation of mammalian cells by plasmid DNA. Molecular and cellular biology. 1987 Aug 1;7(8):2745-52.[2] Tang Y, Dai L, Zhang X, Li J, Hendriks J, Fan X, Gruteser N, Meisenberg A, Baumann A, Katranidis A, Gensch T. SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy. Scientific reports. 2015 Jun 22;5(1):11073