cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8349353
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
DOI: 10.6084/m9.figshare.7386608
title: Additional file 9: of Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition

description: Table S7. Functional characterization and cellular localization of lysine acetylated proteins. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.19445135
title: Additional file 2 of Prognostic significance of SNCA and its methylation in bladder cancer

description: Additional file 2.
DOI: 10.6084/m9.figshare.12101775.v1
title: Additional file 1 of Identification of NHXs in Gossypium species and the positive role of GhNHX1 in salt tolerance

description: Additional file 1: Table S1. Summary of NHXs of G. hirsutum, G. arboreum, and G. raimondii.
DOI: 10.6084/m9.figshare.19445144.v1
title: Additional file 5 of Prognostic significance of SNCA and its methylation in bladder cancer

description: Additional file 5.
DOI: 10.6084/m9.figshare.7386530
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.12101775
title: Additional file 1 of Identification of NHXs in Gossypium species and the positive role of GhNHX1 in salt tolerance

description: Additional file 1: Table S1. Summary of NHXs of G. hirsutum, G. arboreum, and G. raimondii.
DOI: 10.6084/m9.figshare.7386581
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: 10.6084/m9.figshare.12629413
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.7386542.v1
title: Additional file 4: of Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition

description: Table S3. The identified acetylated sites in tea leaves. (XLSX 303 kb)
DOI: 10.35003/yspchc/0ie1xl
title: fig3.pptx

description: :unav
DOI: 10.6084/m9.figshare.12101793.v1
title: Additional file 3 of Identification of NHXs in Gossypium species and the positive role of GhNHX1 in salt tolerance

description: Additional file 3: Table S3. The gene primers used in this study.
DOI: 10.6084/m9.figshare.19969532
title: A phylogeny of Calligonum L. (Polygonaceae) yields challenges to current taxonomic classifications

description: ABSTRACT Calligonum is the only C4 genus within Polygonaceae. We applied DNA sequences from the nuclear ribosomal internal transcribed spacer (nrITS) and five plastid genome regions (psbA-trnH, ycf6-psbM, trnL-F, rpl32-trnL and rbcL) to reconstruct the phylogeny of Calligonum. The nrITS and the combined plastid DNA regions were analysed separately. The phylogeny of the five plastid genome regions supports the treatment of the Calligonum mongolicum complex as a single species with intra-specific geographic structure, and suggests independent hybrid origins for the polyploid species C. caput-medusae and C. arborescens through comparisons with the nrITS tree. We detected phylogenetic incongruence between the nrITS and plastid DNA trees and hypothesized reticulate evolution or hybrid speciation in the genus. Divergence time dating based on nrITS determined that the most recent common ancestor of Calligonum species began diversification 3.46 million years ago [mya; 95 % high probability density (HPD): 1.87-5.71 mya], and diversification began in the Central Asia and China clade ca. 2.68 mya (95 % HPD: 1.28-4.59 mya). We expect that future studies employing next generation sequencing methods, such as RAD-seq, coupled with denser inter- and intra- specific taxonomic sampling, may prove to be cost-effective methods for further investigation of the evolutionary history of this genus.
DOI: 10.6084/m9.figshare.12629452.v1
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.12629461.v1
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.19969532.v1
title: A phylogeny of Calligonum L. (Polygonaceae) yields challenges to current taxonomic classifications

description: ABSTRACT Calligonum is the only C4 genus within Polygonaceae. We applied DNA sequences from the nuclear ribosomal internal transcribed spacer (nrITS) and five plastid genome regions (psbA-trnH, ycf6-psbM, trnL-F, rpl32-trnL and rbcL) to reconstruct the phylogeny of Calligonum. The nrITS and the combined plastid DNA regions were analysed separately. The phylogeny of the five plastid genome regions supports the treatment of the Calligonum mongolicum complex as a single species with intra-specific geographic structure, and suggests independent hybrid origins for the polyploid species C. caput-medusae and C. arborescens through comparisons with the nrITS tree. We detected phylogenetic incongruence between the nrITS and plastid DNA trees and hypothesized reticulate evolution or hybrid speciation in the genus. Divergence time dating based on nrITS determined that the most recent common ancestor of Calligonum species began diversification 3.46 million years ago [mya; 95 % high probability density (HPD): 1.87-5.71 mya], and diversification began in the Central Asia and China clade ca. 2.68 mya (95 % HPD: 1.28-4.59 mya). We expect that future studies employing next generation sequencing methods, such as RAD-seq, coupled with denser inter- and intra- specific taxonomic sampling, may prove to be cost-effective methods for further investigation of the evolutionary history of this genus.
DOI: 10.6084/m9.figshare.25153073
title: ANOVA between froups - Differences between male and female football

description: ANOVA Differences between groups
DOI: 10.6084/m9.figshare.7386608.v1
title: Additional file 9: of Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition

description: Table S7. Functional characterization and cellular localization of lysine acetylated proteins. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.19445213
title: Additional file 2 of miR390 family of Cymbidium goeringii is involved in the development of reproductive organs in transgenic Arabidopsis

description: Additional file 2.
DOI: 10.6084/m9.figshare.19808481
title: Triptolide inhibits oxidative stress and inflammation via the microRNA-155-5p/brain-derived neurotrophic factor to reduce podocyte injury in mice with diabetic nephropathy

description: Diabetic nephropathy (DN) is a complication of diabetes. This study sought to explore the mechanism of triptolide (TP) in podocyte injury in DN. DN mice were induced by high-fat diet&streptozocin and treated with TP. Fasting blood glucose, 24 h urine microalbumin (UMA), the pathological changes of renal tissues, and ultrastructure of renal podocytes were observed. Podocytes (MPC5) were induced by high-glucose (HG) <i>in vitro</i> and treated with TP or microRNA (miR)-155-5p mimics, with Irbesartan as positive control. Reactive oxygen species (ROS) and levels of oxidative stress (OS) and inflammatory factors in MPC5 were detected. The levels of miR-155-5p, podocyte marker protein Nephrin, and inflammatory factors in mice and MPC5 were detected. The targeting relationship between miR-155-5p and brain-derived neurotrophic factor (BDNF) was verified. The expression levels of BDNF were detected. miR-155-5p mimics and overexpressed (oe)-BDNF plasmids were co-transfected into mouse podocytes treated with HG and TP. TP reduced fasting glucose and 24 h UMA of DN mice, alleviated the pathological damage and podocyte injury, up-regulated Nephrin level, and down-regulated miR-155-5p. TP down-regulated the high expression of miR-155-5p in HG-induced MPC5 cells and inhibited HG-induced OS and inflammatory injury, and the improvement effect of TP was better than Irbesartan. Overexpression of miR-155-5p reversed the protective effect of TP on injured mouse podocytes. miR-155-5p targeted BDNF. oe-BDNF reversed the inhibitory effect of oe-miR-155-5p on TP protection on podocyte injury in mice. Overall, TP up-regulated BDNF by inhibiting miR-155-5p, thus inhibiting OS and inflammatory damage and alleviating podocyte injury in DN mice.
DOI: 10.6084/m9.figshare.19445216.v1
title: Additional file 3 of miR390 family of Cymbidium goeringii is involved in the development of reproductive organs in transgenic Arabidopsis

description: Additional file 3.
DOI: 10.6084/m9.figshare.19808481.v1
title: Triptolide inhibits oxidative stress and inflammation via the microRNA-155-5p/brain-derived neurotrophic factor to reduce podocyte injury in mice with diabetic nephropathy

description: Diabetic nephropathy (DN) is a complication of diabetes. This study sought to explore the mechanism of triptolide (TP) in podocyte injury in DN. DN mice were induced by high-fat diet&streptozocin and treated with TP. Fasting blood glucose, 24 h urine microalbumin (UMA), the pathological changes of renal tissues, and ultrastructure of renal podocytes were observed. Podocytes (MPC5) were induced by high-glucose (HG) <i>in vitro</i> and treated with TP or microRNA (miR)-155-5p mimics, with Irbesartan as positive control. Reactive oxygen species (ROS) and levels of oxidative stress (OS) and inflammatory factors in MPC5 were detected. The levels of miR-155-5p, podocyte marker protein Nephrin, and inflammatory factors in mice and MPC5 were detected. The targeting relationship between miR-155-5p and brain-derived neurotrophic factor (BDNF) was verified. The expression levels of BDNF were detected. miR-155-5p mimics and overexpressed (oe)-BDNF plasmids were co-transfected into mouse podocytes treated with HG and TP. TP reduced fasting glucose and 24 h UMA of DN mice, alleviated the pathological damage and podocyte injury, up-regulated Nephrin level, and down-regulated miR-155-5p. TP down-regulated the high expression of miR-155-5p in HG-induced MPC5 cells and inhibited HG-induced OS and inflammatory injury, and the improvement effect of TP was better than Irbesartan. Overexpression of miR-155-5p reversed the protective effect of TP on injured mouse podocytes. miR-155-5p targeted BDNF. oe-BDNF reversed the inhibitory effect of oe-miR-155-5p on TP protection on podocyte injury in mice. Overall, TP up-regulated BDNF by inhibiting miR-155-5p, thus inhibiting OS and inflammatory damage and alleviating podocyte injury in DN mice.
DOI: 10.6084/m9.figshare.19445204
title: Additional file 1 of miR390 family of Cymbidium goeringii is involved in the development of reproductive organs in transgenic Arabidopsis

description: Additional file 1.
DOI: 10.6084/m9.figshare.19445219
title: Additional file 4 of miR390 family of Cymbidium goeringii is involved in the development of reproductive organs in transgenic Arabidopsis

description: Additional file 4.
DOI: 10.6084/m9.figshare.19445204.v1
title: Additional file 1 of miR390 family of Cymbidium goeringii is involved in the development of reproductive organs in transgenic Arabidopsis

description: Additional file 1.
DOI: 10.6084/m9.figshare.19445216
title: Additional file 3 of miR390 family of Cymbidium goeringii is involved in the development of reproductive organs in transgenic Arabidopsis

description: Additional file 3.
DOI: 10.6084/m9.figshare.19445219.v1
title: Additional file 4 of miR390 family of Cymbidium goeringii is involved in the development of reproductive organs in transgenic Arabidopsis

description: Additional file 4.
DOI: 10.6084/m9.figshare.19969647.v1
title: In Silico analysis of Vitis vinifera Cabernet Sauvignon TOR and its responses to sugar and abscisic acid signaling

description: ABSTRACT Target of rapamycin (TOR) is a very critical protein in plants, which connects with biological process, glycometabolism, life span, and photosynthesis. Here, the evolutionary relationship, conserved motif, gene structure and cis-acting elements of TOR were analyzed. Promoter cis-acting elements analysis indicated various cis-acting elements respond to light, auxin, ABA and multiple signal pathway. Transcriptome sequencing and the co-expression network of VvTOR, sugar and abscisic acid (ABA) related genes from Vitis vinifera L. Cabernet Sauvignon berries indicated that VvTOR might participate in sugar and ABA signaling. The expression of VvTOR in grape suspension cells analyzed by quantitative real-time PCR showed that VvTOR responded to ABA and glucose treatment. These results predicted the potential functions of VvTOR in glucose metabolism and ABA signal pathway.
DOI: 10.6084/m9.figshare.12101793
title: Additional file 3 of Identification of NHXs in Gossypium species and the positive role of GhNHX1 in salt tolerance

description: Additional file 3: Table S3. The gene primers used in this study.
DOI: 10.6084/m9.figshare.19969671
title: Reconstruction of the evolutionary biogeography reveals the origin and diversification of Arisaema (Araceae)

description: ABSTRACT Explaining where plants originated and how plants migrated between eastern Asia and other Northern Hemisphere regions is still challenging. The genus Arisaema is considered a good example to illuminate this process, due to its wide distribution in both the tropical and temperate zones. Based on comprehensive taxon sampling, the historical biogeography of Arisaema was conducted using the molecular data from four chloroplast DNA regions. The phylogeny of Arisaema was studied by using ML and BI methods. Divergence times of Arisaema species were estimated by the uncorrelated lognormal Bayesian method. The ancestral area reconstruction of Arisaema was performed with BioGeoBEARS and Bayes-DIVA. Our results indicated that the crown group of Arisaema originated in Southeast Asia ca. 31.28 Ma. After the initial origin, Arisaema was inferred to have become widespread in Southeast Asia. Members in Himalayas, Africa and North China, Japan, the Korean Peninsula region (NJK region) were derived from migrants originating in Southeast Asia. American members were derived from migrants originating in the NJK region. Arisaema originated in Southeast Asia during the Oligocene with the development of tropical rainforest and a warm, moist climate. During the Oligocene to Miocene, Southeast Asia was the original center for the diversification of Arisaema in the NJK region.
DOI: 10.6084/m9.figshare.12101829
title: Additional file 1 of Genome-wide identification of the amino acid permease genes and molecular characterization of their transcriptional responses to various nutrient stresses in allotetraploid rapeseed

description: Additional file 1: Table S1. Molecular characterization of the amino acid permease (AAP) proteins in Brassica napus. Table S2. Differential expression of each amino acid permease (AAP) gene under diverse nutrient stresses. Table S3. Raw expression data for the amino acid permease (AAP) family genes under diverse nutrient stresses. Figure S1. Rooted phylogeny analysis of the AAP genes in allotetraploid rapeseed. Figure S2. Trans-membrane characterization of the amino acid permease (AAP) proteins in Arabidopsis thaliana. The TMHMM (http://www.cbs.dtu.dk/services/TMHMM/) tool was used to predict the transmembrane topology of the AtAAP proteins. Figure S3. Characterization of signal peptides of the amino acid permease (AAP) proteins in Arabidopsis thaliana. The SignalP (http://www.cbs.dtu.dk/services/SignalP/) 4.0 server was used to predict the presence and location of signal peptide cleavage sites in the amino acid sequences of the AtAAP proteins. Figure S4. Tissue-specific expression patterns of the amino acid permease (AAP) genes in Arabidopsis thaliana. (A-H) Relative expression abundances of AtAAP1 (A), AtAAP2 (B), AtAAP3 (C), AtAAP4 (D), AtAAP5 (E), AtAAP6 (F), AtAAP7 (G) and AtAAP8 (H) in various tissues. The red and yellow color indicates relative high and low expression levels of AtAAPs.
DOI: 10.6084/m9.figshare.12101829.v1
title: Additional file 1 of Genome-wide identification of the amino acid permease genes and molecular characterization of their transcriptional responses to various nutrient stresses in allotetraploid rapeseed

description: Additional file 1: Table S1. Molecular characterization of the amino acid permease (AAP) proteins in Brassica napus. Table S2. Differential expression of each amino acid permease (AAP) gene under diverse nutrient stresses. Table S3. Raw expression data for the amino acid permease (AAP) family genes under diverse nutrient stresses. Figure S1. Rooted phylogeny analysis of the AAP genes in allotetraploid rapeseed. Figure S2. Trans-membrane characterization of the amino acid permease (AAP) proteins in Arabidopsis thaliana. The TMHMM (http://www.cbs.dtu.dk/services/TMHMM/) tool was used to predict the transmembrane topology of the AtAAP proteins. Figure S3. Characterization of signal peptides of the amino acid permease (AAP) proteins in Arabidopsis thaliana. The SignalP (http://www.cbs.dtu.dk/services/SignalP/) 4.0 server was used to predict the presence and location of signal peptide cleavage sites in the amino acid sequences of the AtAAP proteins. Figure S4. Tissue-specific expression patterns of the amino acid permease (AAP) genes in Arabidopsis thaliana. (A-H) Relative expression abundances of AtAAP1 (A), AtAAP2 (B), AtAAP3 (C), AtAAP4 (D), AtAAP5 (E), AtAAP6 (F), AtAAP7 (G) and AtAAP8 (H) in various tissues. The red and yellow color indicates relative high and low expression levels of AtAAPs.
DOI: 10.6084/m9.figshare.19445492
title: Additional file 4 of Integrative analysis of DNA methylation and gene expression reveals key molecular signatures in acute myocardial infarction

description: Additional file 4. Differential expressed genes regulated by DNA methylation.
DOI: 10.6084/m9.figshare.19445489.v1
title: Additional file 3 of Integrative analysis of DNA methylation and gene expression reveals key molecular signatures in acute myocardial infarction

description: Additional file 3. Differential expressed genes.
DOI: 10.6084/m9.figshare.19445492.v1
title: Additional file 4 of Integrative analysis of DNA methylation and gene expression reveals key molecular signatures in acute myocardial infarction

description: Additional file 4. Differential expressed genes regulated by DNA methylation.
DOI: 10.6084/m9.figshare.19969647
title: In Silico analysis of Vitis vinifera Cabernet Sauvignon TOR and its responses to sugar and abscisic acid signaling

description: ABSTRACT Target of rapamycin (TOR) is a very critical protein in plants, which connects with biological process, glycometabolism, life span, and photosynthesis. Here, the evolutionary relationship, conserved motif, gene structure and cis-acting elements of TOR were analyzed. Promoter cis-acting elements analysis indicated various cis-acting elements respond to light, auxin, ABA and multiple signal pathway. Transcriptome sequencing and the co-expression network of VvTOR, sugar and abscisic acid (ABA) related genes from Vitis vinifera L. Cabernet Sauvignon berries indicated that VvTOR might participate in sugar and ABA signaling. The expression of VvTOR in grape suspension cells analyzed by quantitative real-time PCR showed that VvTOR responded to ABA and glucose treatment. These results predicted the potential functions of VvTOR in glucose metabolism and ABA signal pathway.
DOI: 10.6084/m9.figshare.19969671.v1
title: Reconstruction of the evolutionary biogeography reveals the origin and diversification of Arisaema (Araceae)

description: ABSTRACT Explaining where plants originated and how plants migrated between eastern Asia and other Northern Hemisphere regions is still challenging. The genus Arisaema is considered a good example to illuminate this process, due to its wide distribution in both the tropical and temperate zones. Based on comprehensive taxon sampling, the historical biogeography of Arisaema was conducted using the molecular data from four chloroplast DNA regions. The phylogeny of Arisaema was studied by using ML and BI methods. Divergence times of Arisaema species were estimated by the uncorrelated lognormal Bayesian method. The ancestral area reconstruction of Arisaema was performed with BioGeoBEARS and Bayes-DIVA. Our results indicated that the crown group of Arisaema originated in Southeast Asia ca. 31.28 Ma. After the initial origin, Arisaema was inferred to have become widespread in Southeast Asia. Members in Himalayas, Africa and North China, Japan, the Korean Peninsula region (NJK region) were derived from migrants originating in Southeast Asia. American members were derived from migrants originating in the NJK region. Arisaema originated in Southeast Asia during the Oligocene with the development of tropical rainforest and a warm, moist climate. During the Oligocene to Miocene, Southeast Asia was the original center for the diversification of Arisaema in the NJK region.
DOI: 10.6084/m9.figshare.19445489
title: Additional file 3 of Integrative analysis of DNA methylation and gene expression reveals key molecular signatures in acute myocardial infarction

description: Additional file 3. Differential expressed genes.
DOI: 10.6084/m9.figshare.19445290.v1
title: Additional file 2 of Analysis of the genotype–phenotype correlation of MYO15A variants in Chinese non-syndromic hearing loss patients

description: Additional file 2. Table S2 Primer sets of Sanger sequencing used in this study.
DOI: 10.6084/m9.figshare.19445287.v1
title: Additional file 1 of Analysis of the genotype–phenotype correlation of MYO15A variants in Chinese non-syndromic hearing loss patients

description: Additional file 1 Table S1 List of the 168 deafness genes and miRNA.