cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6224354
title: Additional file 1: of Long non-coding RNAs of switchgrass (Panicum virgatum L.) in multiple dehydration stresses

description: Figure S1. Overview of the RNA-Seq results and repeatability of different biological replicates. The first eight figures show the proportion of clean reads in the sequenced samples; the next three figures show the repeated expression of genes in two biological replicates; the last eight figures showed the correlations between differentially expressed genes in two biological replicates, and the distributions of upregulated and downregulated genes/lncRNAs in multiple dehydration stresses. C, control; D1–2, the first and second dehydration stresses; R1, the first recovery period. Figure S2. Water loss and survive rates in multiple dehydration stresses. A. Water loss from leaves during the first, second and third dehydration stresses. B. Survival rates of trained and non-trained switchgrass. Figure S3. Verification of four types of dehydration memory genes by quantitative real-time PCR. C, control; D1–2, first and second dehydration stresses; R1, first recovery period. Relative gene expressed levels were calculated using the ΔΔCT method with PveEF-1α as the internal control, and three biological replicates were performed for each experiment. (ZIP 1905 kb)
DOI: 10.6084/m9.figshare.6224354.v1
title: Additional file 1: of Long non-coding RNAs of switchgrass (Panicum virgatum L.) in multiple dehydration stresses

description: Figure S1. Overview of the RNA-Seq results and repeatability of different biological replicates. The first eight figures show the proportion of clean reads in the sequenced samples; the next three figures show the repeated expression of genes in two biological replicates; the last eight figures showed the correlations between differentially expressed genes in two biological replicates, and the distributions of upregulated and downregulated genes/lncRNAs in multiple dehydration stresses. C, control; D1–2, the first and second dehydration stresses; R1, the first recovery period. Figure S2. Water loss and survive rates in multiple dehydration stresses. A. Water loss from leaves during the first, second and third dehydration stresses. B. Survival rates of trained and non-trained switchgrass. Figure S3. Verification of four types of dehydration memory genes by quantitative real-time PCR. C, control; D1–2, first and second dehydration stresses; R1, first recovery period. Relative gene expressed levels were calculated using the ΔΔCT method with PveEF-1α as the internal control, and three biological replicates were performed for each experiment. (ZIP 1905 kb)
DOI: 10.6084/m9.figshare.6224372
title: Additional file 2: of Long non-coding RNAs of switchgrass (Panicum virgatum L.) in multiple dehydration stresses

description: Table S1. List of memory lncRNAs. Table S2. Primers used in qRT-PCR. Table S3. Expression summary of different samples and treatments. Table S4. List of differentially expressed lncRNAs. Table S5. LncRNAs annotated by antisense and upstream or downstream. Table S6. Differentially expressed lncRNAs and the annotated genes. Table S7. Differentially expressed lncRNAs annotated with differentially expressed genes. Table S8. GO term _ response to stress. Table S9. Top 20 pathway enriched in annotation genes. Table S10. LncRNAs and genes involved in ABA biosynthesis and signal transduction. Table S11. LncRNAs and genes involved in ETH biosynthesis and signal transduction. Table S12. LncRNAs and genes involved in starch and sucrose metabolism. Table S13. Dehydration response and transcriptional memory genes or lncRNAs in switchgrass, maize and Arabidopsis. (ZIP 3778Â kb)
DOI: 10.6084/m9.figshare.6224372.v1
title: Additional file 2: of Long non-coding RNAs of switchgrass (Panicum virgatum L.) in multiple dehydration stresses

description: Table S1. List of memory lncRNAs. Table S2. Primers used in qRT-PCR. Table S3. Expression summary of different samples and treatments. Table S4. List of differentially expressed lncRNAs. Table S5. LncRNAs annotated by antisense and upstream or downstream. Table S6. Differentially expressed lncRNAs and the annotated genes. Table S7. Differentially expressed lncRNAs annotated with differentially expressed genes. Table S8. GO term _ response to stress. Table S9. Top 20 pathway enriched in annotation genes. Table S10. LncRNAs and genes involved in ABA biosynthesis and signal transduction. Table S11. LncRNAs and genes involved in ETH biosynthesis and signal transduction. Table S12. LncRNAs and genes involved in starch and sucrose metabolism. Table S13. Dehydration response and transcriptional memory genes or lncRNAs in switchgrass, maize and Arabidopsis. (ZIP 3778Â kb)
DOI: 10.6084/m9.figshare.6224381
title: Additional file 10: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: RT-PCR primer information and relative expression values. (XLSX 107Â kb)
DOI: 10.6084/m9.figshare.6224381.v1
title: Additional file 10: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: RT-PCR primer information and relative expression values. (XLSX 107Â kb)
DOI: 10.6084/m9.figshare.6224396
title: Additional file 1: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: High-throughput sequencing data and tissue information. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6224396.v1
title: Additional file 1: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: High-throughput sequencing data and tissue information. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6224414
title: Additional file 2: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: Candidate lincRNA information. (XLSX 2776Â kb)
DOI: 10.6084/m9.figshare.6224414.v1
title: Additional file 2: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: Candidate lincRNA information. (XLSX 2776Â kb)
DOI: 10.6084/m9.figshare.6224423
title: Additional file 3: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: Candidate ancRNA information. (XLSX 330Â kb)
DOI: 10.6084/m9.figshare.6224423.v1
title: Additional file 3: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: Candidate ancRNA information. (XLSX 330Â kb)
DOI: 10.6084/m9.figshare.6224441
title: Additional file 4: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: Candidate sense lncRNA information. (XLSX 33Â kb)
DOI: 10.6084/m9.figshare.6224441.v1
title: Additional file 4: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: Candidate sense lncRNA information. (XLSX 33Â kb)
DOI: 10.6084/m9.figshare.6224450
title: Additional file 1: of Proteomics integrated with metabolomics: analysis of the internal causes of nutrient changes in alfalfa at different growth stages

description: Table S1. Protein quantification and analysis of significant differences. (XLSX 81Â kb)
DOI: 10.6084/m9.figshare.6224450.v1
title: Additional file 1: of Proteomics integrated with metabolomics: analysis of the internal causes of nutrient changes in alfalfa at different growth stages

description: Table S1. Protein quantification and analysis of significant differences. (XLSX 81Â kb)
DOI: 10.6084/m9.figshare.6224453
title: Additional file 5: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: Normalized lincRNA expression values across 3 developmental stages. (XLSX 405Â kb)
DOI: 10.6084/m9.figshare.6224453.v1
title: Additional file 5: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: Normalized lincRNA expression values across 3 developmental stages. (XLSX 405Â kb)
DOI: 10.6084/m9.figshare.6224465
title: Additional file 6: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: Statistical analysis of lincRNA expression levels in the MG versus BR stage. (XLSX 53Â kb)
DOI: 10.6084/m9.figshare.6224465.v1
title: Additional file 6: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: Statistical analysis of lincRNA expression levels in the MG versus BR stage. (XLSX 53Â kb)
DOI: 10.6084/m9.figshare.6224471
title: Additional file 2: of Proteomics integrated with metabolomics: analysis of the internal causes of nutrient changes in alfalfa at different growth stages

description: Table S2. KEGG pathways in which differentially expressed proteins are involved. (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.6224471.v1
title: Additional file 2: of Proteomics integrated with metabolomics: analysis of the internal causes of nutrient changes in alfalfa at different growth stages

description: Table S2. KEGG pathways in which differentially expressed proteins are involved. (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.6224474
title: Additional file 7: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: Statistical analysis of lincRNA expression levels in the MG versus BR + 7 stage. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.6224474.v1
title: Additional file 7: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: Statistical analysis of lincRNA expression levels in the MG versus BR + 7 stage. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.6224486
title: Additional file 3: of Proteomics integrated with metabolomics: analysis of the internal causes of nutrient changes in alfalfa at different growth stages

description: Table S3. Proteome-metabolome data co-analysis. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.6224486.v1
title: Additional file 3: of Proteomics integrated with metabolomics: analysis of the internal causes of nutrient changes in alfalfa at different growth stages

description: Table S3. Proteome-metabolome data co-analysis. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.6224489
title: Additional file 8: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: Statistical analysis of lincRNA expression levels in the BR versus BR + 7 stage. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.6224489.v1
title: Additional file 8: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: Statistical analysis of lincRNA expression levels in the BR versus BR + 7 stage. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.6224495
title: Additional file 9: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: Information regarding co-regulated lincRNA and mRNA pairs and corresponding correlation. (XLSX 31Â kb)
DOI: 10.6084/m9.figshare.6224495.v1
title: Additional file 9: of Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

description: Information regarding co-regulated lincRNA and mRNA pairs and corresponding correlation. (XLSX 31Â kb)
DOI: 10.6084/m9.figshare.6225209
title: Supplementary Table S1 for: Therapeutic potential of human adipose-derived stem cell exosomes in stress urinary incontinence – an in vitro and in vivo study

description: Results of GO analysis<b>Background/Aims:
</b>To
evaluate whether local injection of exosomes derived from human adipose-derived
stem cells (hADSCs) facilitates recovery of stress urinary incontinence (SUI)
in a rat model.

<b>Methods:</b> For the in vitro
study, a Cell Counting Kit-8 (CCK-8) array and proteomic analysis were
performed. For the in vivo study, female rats were divided into four groups:
sham, SUI, adipose-derived stem cell (ADSC), and exosomes (<i>n</i> = 12 each). The SUI model was generated by pudendal nerve
transection and vaginal dilation. Vehicle, hADSCs, or exosomes were injected
into the peripheral urethra. After 2, 4, and 8 weeks, the rats underwent cystometrography
and leak point pressure (LPP) testing, and tissues were harvested for
histochemical analyses.

<b>Results:</b> The CCK-8
experiment demonstrated that ADSC-derived exosomes could enhance the growth of
skeletal muscle and Schwann cell lines in a dose-dependent manner. Proteomic
analysis revealed that ADSC-derived exosomes contained various proteins of
different signaling pathways. Some of these proteins are associated with the
PI3K-Akt, Jak-STAT, and Wnt pathways, which are related to skeletal muscle and
nerve regeneration and proliferation. In vivo experiments illustrated that rats
of the exosome group had higher bladder capacity and LPP, and had more striated
muscle fibers and peripheral nerve fibers in the urethra than rats of the SUI
group. Both urethral function and histology of rats in the exosome group were
slightly better than those in the ADSC group. 

<b>Conclusions:</b> Local injection of
hADSC-derived exosomes improved functional and histological recovery after SUI.
DOI: 10.6084/m9.figshare.6225209.v1
title: Table S1

description: Results of GO analysis
DOI: 10.6084/m9.figshare.6225209.v3
title: Supplementary Table S1 for: Therapeutic potential of human adipose-derived stem cell exosomes in stress urinary incontinence – an in vitro and in vivo study

description: Results of GO analysis<b>Background/Aims:
</b>To
evaluate whether local injection of exosomes derived from human adipose-derived
stem cells (hADSCs) facilitates recovery of stress urinary incontinence (SUI)
in a rat model.

<b>Methods:</b> For the in vitro
study, a Cell Counting Kit-8 (CCK-8) array and proteomic analysis were
performed. For the in vivo study, female rats were divided into four groups:
sham, SUI, adipose-derived stem cell (ADSC), and exosomes (<i>n</i> = 12 each). The SUI model was generated by pudendal nerve
transection and vaginal dilation. Vehicle, hADSCs, or exosomes were injected
into the peripheral urethra. After 2, 4, and 8 weeks, the rats underwent cystometrography
and leak point pressure (LPP) testing, and tissues were harvested for
histochemical analyses.

<b>Results:</b> The CCK-8
experiment demonstrated that ADSC-derived exosomes could enhance the growth of
skeletal muscle and Schwann cell lines in a dose-dependent manner. Proteomic
analysis revealed that ADSC-derived exosomes contained various proteins of
different signaling pathways. Some of these proteins are associated with the
PI3K-Akt, Jak-STAT, and Wnt pathways, which are related to skeletal muscle and
nerve regeneration and proliferation. In vivo experiments illustrated that rats
of the exosome group had higher bladder capacity and LPP, and had more striated
muscle fibers and peripheral nerve fibers in the urethra than rats of the SUI
group. Both urethral function and histology of rats in the exosome group were
slightly better than those in the ADSC group. 

<b>Conclusions:</b> Local injection of
hADSC-derived exosomes improved functional and histological recovery after SUI.
DOI: 10.6084/m9.figshare.6225209.v2
title: Supplementary Table S1: Therapeutic potential of human adipose-derived stem cell exosomes in stress urinary incontinence – an in vitro and in vivo study

description: Results of GO analysis<b>Background/Aims:
</b>To
evaluate whether local injection of exosomes derived from human adipose-derived
stem cells (hADSCs) facilitates recovery of stress urinary incontinence (SUI)
in a rat model.

<b>Methods:</b> For the in vitro
study, a Cell Counting Kit-8 (CCK-8) array and proteomic analysis were
performed. For the in vivo study, female rats were divided into four groups:
sham, SUI, adipose-derived stem cell (ADSC), and exosomes (<i>n</i> = 12 each). The SUI model was generated by pudendal nerve
transection and vaginal dilation. Vehicle, hADSCs, or exosomes were injected
into the peripheral urethra. After 2, 4, and 8 weeks, the rats underwent cystometrography
and leak point pressure (LPP) testing, and tissues were harvested for
histochemical analyses.

<b>Results:</b> The CCK-8
experiment demonstrated that ADSC-derived exosomes could enhance the growth of
skeletal muscle and Schwann cell lines in a dose-dependent manner. Proteomic
analysis revealed that ADSC-derived exosomes contained various proteins of
different signaling pathways. Some of these proteins are associated with the
PI3K-Akt, Jak-STAT, and Wnt pathways, which are related to skeletal muscle and
nerve regeneration and proliferation. In vivo experiments illustrated that rats
of the exosome group had higher bladder capacity and LPP, and had more striated
muscle fibers and peripheral nerve fibers in the urethra than rats of the SUI
group. Both urethral function and histology of rats in the exosome group were
slightly better than those in the ADSC group. 

<b>Conclusions:</b> Local injection of
hADSC-derived exosomes improved functional and histological recovery after SUI.
DOI: 10.6084/m9.figshare.6225212
title: Supplementary Table S2 for: Therapeutic potential of human adipose-derived stem cell exosomes in stress urinary incontinence – an in vitro and in vivo study

description: The results of KEGG pathway analysis<b>Background/Aims:
</b>To
evaluate whether local injection of exosomes derived from human adipose-derived
stem cells (hADSCs) facilitates recovery of stress urinary incontinence (SUI)
in a rat model.

<b>Methods:</b> For the in vitro
study, a Cell Counting Kit-8 (CCK-8) array and proteomic analysis were
performed. For the in vivo study, female rats were divided into four groups:
sham, SUI, adipose-derived stem cell (ADSC), and exosomes (<i>n</i> = 12 each). The SUI model was generated by pudendal nerve
transection and vaginal dilation. Vehicle, hADSCs, or exosomes were injected
into the peripheral urethra. After 2, 4, and 8 weeks, the rats underwent cystometrography
and leak point pressure (LPP) testing, and tissues were harvested for
histochemical analyses.

<b>Results:</b> The CCK-8
experiment demonstrated that ADSC-derived exosomes could enhance the growth of
skeletal muscle and Schwann cell lines in a dose-dependent manner. Proteomic
analysis revealed that ADSC-derived exosomes contained various proteins of
different signaling pathways. Some of these proteins are associated with the
PI3K-Akt, Jak-STAT, and Wnt pathways, which are related to skeletal muscle and
nerve regeneration and proliferation. In vivo experiments illustrated that rats
of the exosome group had higher bladder capacity and LPP, and had more striated
muscle fibers and peripheral nerve fibers in the urethra than rats of the SUI
group. Both urethral function and histology of rats in the exosome group were
slightly better than those in the ADSC group. 

<b>Conclusions:</b> Local injection of
hADSC-derived exosomes improved functional and histological recovery after SUI.
DOI: 10.6084/m9.figshare.6225212.v1
title: Table S2

description: The results of KEGG pathway analysis
DOI: 10.6084/m9.figshare.6225212.v2
title: Table S2 for: Therapeutic potential of human adipose-derived stem cell exosomes in stress urinary incontinence – an in vitro and in vivo study

description: The results of KEGG pathway analysis<b>Background/Aims:
</b>To
evaluate whether local injection of exosomes derived from human adipose-derived
stem cells (hADSCs) facilitates recovery of stress urinary incontinence (SUI)
in a rat model.

<b>Methods:</b> For the in vitro
study, a Cell Counting Kit-8 (CCK-8) array and proteomic analysis were
performed. For the in vivo study, female rats were divided into four groups:
sham, SUI, adipose-derived stem cell (ADSC), and exosomes (<i>n</i> = 12 each). The SUI model was generated by pudendal nerve
transection and vaginal dilation. Vehicle, hADSCs, or exosomes were injected
into the peripheral urethra. After 2, 4, and 8 weeks, the rats underwent cystometrography
and leak point pressure (LPP) testing, and tissues were harvested for
histochemical analyses.

<b>Results:</b> The CCK-8
experiment demonstrated that ADSC-derived exosomes could enhance the growth of
skeletal muscle and Schwann cell lines in a dose-dependent manner. Proteomic
analysis revealed that ADSC-derived exosomes contained various proteins of
different signaling pathways. Some of these proteins are associated with the
PI3K-Akt, Jak-STAT, and Wnt pathways, which are related to skeletal muscle and
nerve regeneration and proliferation. In vivo experiments illustrated that rats
of the exosome group had higher bladder capacity and LPP, and had more striated
muscle fibers and peripheral nerve fibers in the urethra than rats of the SUI
group. Both urethral function and histology of rats in the exosome group were
slightly better than those in the ADSC group. 

<b>Conclusions:</b> Local injection of
hADSC-derived exosomes improved functional and histological recovery after SUI.
DOI: 10.6084/m9.figshare.6225212.v3
title: Supplementary Table S2 for: Therapeutic potential of human adipose-derived stem cell exosomes in stress urinary incontinence – an in vitro and in vivo study

description: The results of KEGG pathway analysis<b>Background/Aims:
</b>To
evaluate whether local injection of exosomes derived from human adipose-derived
stem cells (hADSCs) facilitates recovery of stress urinary incontinence (SUI)
in a rat model.

<b>Methods:</b> For the in vitro
study, a Cell Counting Kit-8 (CCK-8) array and proteomic analysis were
performed. For the in vivo study, female rats were divided into four groups:
sham, SUI, adipose-derived stem cell (ADSC), and exosomes (<i>n</i> = 12 each). The SUI model was generated by pudendal nerve
transection and vaginal dilation. Vehicle, hADSCs, or exosomes were injected
into the peripheral urethra. After 2, 4, and 8 weeks, the rats underwent cystometrography
and leak point pressure (LPP) testing, and tissues were harvested for
histochemical analyses.

<b>Results:</b> The CCK-8
experiment demonstrated that ADSC-derived exosomes could enhance the growth of
skeletal muscle and Schwann cell lines in a dose-dependent manner. Proteomic
analysis revealed that ADSC-derived exosomes contained various proteins of
different signaling pathways. Some of these proteins are associated with the
PI3K-Akt, Jak-STAT, and Wnt pathways, which are related to skeletal muscle and
nerve regeneration and proliferation. In vivo experiments illustrated that rats
of the exosome group had higher bladder capacity and LPP, and had more striated
muscle fibers and peripheral nerve fibers in the urethra than rats of the SUI
group. Both urethral function and histology of rats in the exosome group were
slightly better than those in the ADSC group. 

<b>Conclusions:</b> Local injection of
hADSC-derived exosomes improved functional and histological recovery after SUI.
DOI: 10.6084/m9.figshare.6225560
title: Liver fat depot in inflammatory bowel disease: influenced mainly by nutrition and indicates endoscopic activity

description: This is the original dataset for an research paper.
DOI: 10.6084/m9.figshare.6225560.v1
title: Liver fat depot in inflammatory bowel disease: influenced mainly by nutrition and indicates endoscopic activity

description: This is the original dataset for an research paper.