cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7435331
title: Supplementary Material for: circZMYM2 Competed Endogenously with miR-335-5p to Regulate JMJD2C in Pancreatic Cancer

description: <b><i>Background/Aims:</i></b> We aimed to study the involvement of circZMYM2 (hsa_circ_0099999) in pancreatic cancer (PC) cell proliferation, apoptosis and invasion and to figured out the underlying mechanism of circZMYM2 regulating miR-335-5p and <i>JMJD2C</i>. <b><i>Methods:</i></b> CircRNA differential expressions in twenty PC samples and paired normal tissue samples were analyzed using Arraystar Human CircRNA microarray V1. CircZMYM2 expression level was determined via qRT-PCR. The effects of circZMYM2 inhibition and overexpression on cell proliferation, cell apoptosis and cell invasion were investigated by CCK-8 assays, Flow cytometry assays and Transwell assays. An animal experiment on nude mice was put forward to test the influence of circZMYM2 knockdown on tumor growth. The relationship between circZMYM2, miR-335 and JMJD2C was verified by RNA pull down, dual-luciferase reporter assays and rescue experiment. The effect of circZMYM2 and miR-335-5p on the expression of JMJD2C protein was detected by western blot. <b><i>Results:</i></b> CircZMYM2 overexpression was observed in both PC tissues and cells. Knockdown of circZMYM2 inhibited proliferation, induced apoptosis, and weakened invasion ability of cancer cells. Tumor growth was restrained <i>in vivo</i>. CircZMYM2 repressed the expression of its target miR-335-5p. MiR-335-5p attenuated pancreatic cancer development via inhibition of <i>JMJD2C</i>. <b><i>Conclusion:</i></b> Our study demonstrated that circZMYM2 promoted PC progression. CircZMYM2 had a sponge effect on miR-335-5p and modulated the downstream oncogene <i>JMJD2C</i>.
DOI: 10.7284/135292
title: Meteorological Station data collected during research cruise NA089 using a Coastal Weatherpak-2000 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435331.v1
title: Supplementary Material for: circZMYM2 Competed Endogenously with miR-335-5p to Regulate JMJD2C in Pancreatic Cancer

description: <b><i>Background/Aims:</i></b> We aimed to study the involvement of circZMYM2 (hsa_circ_0099999) in pancreatic cancer (PC) cell proliferation, apoptosis and invasion and to figured out the underlying mechanism of circZMYM2 regulating miR-335-5p and <i>JMJD2C</i>. <b><i>Methods:</i></b> CircRNA differential expressions in twenty PC samples and paired normal tissue samples were analyzed using Arraystar Human CircRNA microarray V1. CircZMYM2 expression level was determined via qRT-PCR. The effects of circZMYM2 inhibition and overexpression on cell proliferation, cell apoptosis and cell invasion were investigated by CCK-8 assays, Flow cytometry assays and Transwell assays. An animal experiment on nude mice was put forward to test the influence of circZMYM2 knockdown on tumor growth. The relationship between circZMYM2, miR-335 and JMJD2C was verified by RNA pull down, dual-luciferase reporter assays and rescue experiment. The effect of circZMYM2 and miR-335-5p on the expression of JMJD2C protein was detected by western blot. <b><i>Results:</i></b> CircZMYM2 overexpression was observed in both PC tissues and cells. Knockdown of circZMYM2 inhibited proliferation, induced apoptosis, and weakened invasion ability of cancer cells. Tumor growth was restrained <i>in vivo</i>. CircZMYM2 repressed the expression of its target miR-335-5p. MiR-335-5p attenuated pancreatic cancer development via inhibition of <i>JMJD2C</i>. <b><i>Conclusion:</i></b> Our study demonstrated that circZMYM2 promoted PC progression. CircZMYM2 had a sponge effect on miR-335-5p and modulated the downstream oncogene <i>JMJD2C</i>.
DOI: 10.7284/136022
title: Multibeam Echosounder data collected during research cruise NA089 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/136023
title: Multibeam Echosounder data collected during research cruise NA089 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/135289
title: Singlebeam Echosounder data collected during research cruise NA089 using a Knudsen 3260 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/135287
title: SSV (Sound Speed Velocimeter) data collected during research cruise NA089 using a AML SV Xchange instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/135244
title: Expendable Probe data collected during research cruise NA090 using a Sippican MK21 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435274
title: Encapsulation of <i>S</i>-nitrosoglutathione: a transcriptomic validation

description: <b>Objective:</b><i>S</i>-nitrosogluthatione (GSNO), a <i>S</i>-nitrosothiol, is a commonly used as nitric oxide (NO<sup>•</sup>) donor. However, its half-life is too short for a direct therapeutic use. To protect and ensure a sustained release of NO<sup>•</sup>, the encapsulation of GSNO into nanoparticles may be an interesting option. <b>Methods:</b> In this work, we have investigated the early (4 h) and late (24 h) transcriptomic response of THP-1 human monocytes cells to two doses (1.4 and 6 µM) of either free or Eudragit<sup>®</sup> nano-encapsulated GSNO using RNA microarray. <b>Results:</b> After exposure to free GSNO, genes mainly involved in apoptosis, cell differentiation, immune response and metabolic processes were differentially expressed. Although, cells exposed to free or encapsulated GSNO behave differently, activation of genes involved in blood coagulation, immune response and cell cycle was observed in both conditions. <b>Conclusions:</b> These results suggest that the encapsulation of low doses of GSNO into Eudragit<sup>®</sup> nanoparticles leads to a progressive release of GSNO making this compound a possible oral therapy for several biomedical applications like inflammatory bowel diseases.
DOI: 10.7284/135242
title: INS (Inertial Navigation System) data collected during research cruise NA090 using a Kongsberg Seatex MRU-5 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435274.v2
title: Encapsulation of <i>S</i>-nitrosoglutathione: a transcriptomic validation

description: <b>Objective:</b><i>S</i>-nitrosogluthatione (GSNO), a <i>S</i>-nitrosothiol, is a commonly used as nitric oxide (NO<sup>•</sup>) donor. However, its half-life is too short for a direct therapeutic use. To protect and ensure a sustained release of NO<sup>•</sup>, the encapsulation of GSNO into nanoparticles may be an interesting option. <b>Methods:</b> In this work, we have investigated the early (4 h) and late (24 h) transcriptomic response of THP-1 human monocytes cells to two doses (1.4 and 6 µM) of either free or Eudragit<sup>®</sup> nano-encapsulated GSNO using RNA microarray. <b>Results:</b> After exposure to free GSNO, genes mainly involved in apoptosis, cell differentiation, immune response and metabolic processes were differentially expressed. Although, cells exposed to free or encapsulated GSNO behave differently, activation of genes involved in blood coagulation, immune response and cell cycle was observed in both conditions. <b>Conclusions:</b> These results suggest that the encapsulation of low doses of GSNO into Eudragit<sup>®</sup> nanoparticles leads to a progressive release of GSNO making this compound a possible oral therapy for several biomedical applications like inflammatory bowel diseases.
DOI: 10.7284/135245
title: INS (Inertial Navigation System) data collected during research cruise NA090 using a Kongsberg Seapath 330+ instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435250
title: MASSIVE viewer

description: Files for a website that explains a novel methodology for sensitivity analysis of agent-based simulation, MASSIVE (Massively parallel Agent-based Simulations and Subsequent Interactive Visualization-based Exploration). <br>
DOI: 10.6084/m9.figshare.7435274.v1
title: Encapsulation of <i>S</i>-nitrosoglutathione: a transcriptomic validation

description: <b>Objective:</b><i>S</i>-nitrosogluthatione (GSNO), a <i>S</i>-nitrosothiol, is a commonly used as nitric oxide (NO<sup>•</sup>) donor. However, its half-life is too short for a direct therapeutic use. To protect and ensure a sustained release of NO<sup>•</sup>, the encapsulation of GSNO into nanoparticles may be an interesting option. <b>Methods:</b> In this work, we have investigated the early (4 h) and late (24 h) transcriptomic response of THP-1 human monocytes cells to two doses (1.4 and 6 µM) of either free or Eudragit<sup>®</sup> nano-encapsulated GSNO using RNA microarray. <b>Results:</b> After exposure to free GSNO, genes mainly involved in apoptosis, cell differentiation, immune response and metabolic processes were differentially expressed. Although, cells exposed to free or encapsulated GSNO behave differently, activation of genes involved in blood coagulation, immune response and cell cycle was observed in both conditions. <b>Conclusions:</b> These results suggest that the encapsulation of low doses of GSNO into Eudragit<sup>®</sup> nanoparticles leads to a progressive release of GSNO making this compound a possible oral therapy for several biomedical applications like inflammatory bowel diseases.
DOI: 10.6084/m9.figshare.7435250.v2
title: MASSIVE viewer

description: Files for a website that explains a novel methodology for sensitivity analysis of agent-based simulation, MASSIVE (Massively parallel Agent-based Simulations and Subsequent Interactive Visualization-based Exploration). <br>
DOI: 10.7284/135246
title: Meteorological Station data collected during research cruise NA090 using a Coastal Weatherpak-2000 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435250.v1
title: MASSIVE viewer

description: Files for a website that explains a novel methodology for sensitivity analysis of agent-based simulation, MASSIVE (Massively parallel Agent-based Simulations and Subsequent Interactive Visualization-based Exploration). <br>
DOI: 10.7284/136024
title: Multibeam Echosounder data collected during research cruise NA090 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435229
title: Supplementary Data from Avoided emissions and conservation of scrub mangroves: potential for a Blue Carbon project in the Gulf of California, Mexico

description: Mangroves are considered ideal ecosystems for Blue Carbon projects. However, because of their short stature, some mangroves (‘scrub’ mangroves, less than 2 m) do not fulfil the current definition of ‘forests’ which makes them ineligible for emission reduction programmes such as REDD+. Short stature mangroves can be the dominant form of mangroves in arid and poor nutrient landscapes, and emissions from their deforestation and degradation could be substantial. Here, we describe a potential Blue Carbon project in the Gulf of California, Mexico, to illustrate that projects which avoid emissions from deforestation and degradation could provide financial resources to protect mangroves that cannot be included in other emission reduction programmes. The goal of the project is to protect 16 058 ha of mangroves through conservation concessions from the Mexican Federal Government. The cumulative avoided emissions of the project are 2.84 million Mg CO<sub>2</sub> over 100 years, valued at $US 426 000 per year (US$15 per Mg CO<sub>2 </sub>in the California market). The funds could be used for community-based projects that will improve mangrove management, such as surveillance, eradication of invasive species, rehabilitation after tropical storms and environmental education. The strong institutional support, secure financial status, community engagement and clear project boundaries provide favourable conditions to implement this Blue Carbon project. Financial resources from Blue Carbon projects, even in mangroves of short stature, can provide substantial resources to enhance community resilience and mangrove protection.
DOI: 10.7284/136025
title: Multibeam Echosounder data collected during research cruise NA090 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435229.v1
title: Supplementary Data from Avoided emissions and conservation of scrub mangroves: potential for a Blue Carbon project in the Gulf of California, Mexico

description: Mangroves are considered ideal ecosystems for Blue Carbon projects. However, because of their short stature, some mangroves (‘scrub’ mangroves, less than 2 m) do not fulfil the current definition of ‘forests’ which makes them ineligible for emission reduction programmes such as REDD+. Short stature mangroves can be the dominant form of mangroves in arid and poor nutrient landscapes, and emissions from their deforestation and degradation could be substantial. Here, we describe a potential Blue Carbon project in the Gulf of California, Mexico, to illustrate that projects which avoid emissions from deforestation and degradation could provide financial resources to protect mangroves that cannot be included in other emission reduction programmes. The goal of the project is to protect 16 058 ha of mangroves through conservation concessions from the Mexican Federal Government. The cumulative avoided emissions of the project are 2.84 million Mg CO<sub>2</sub> over 100 years, valued at $US 426 000 per year (US$15 per Mg CO<sub>2 </sub>in the California market). The funds could be used for community-based projects that will improve mangrove management, such as surveillance, eradication of invasive species, rehabilitation after tropical storms and environmental education. The strong institutional support, secure financial status, community engagement and clear project boundaries provide favourable conditions to implement this Blue Carbon project. Financial resources from Blue Carbon projects, even in mangroves of short stature, can provide substantial resources to enhance community resilience and mangrove protection.
DOI: 10.7284/135243
title: Singlebeam Echosounder data collected during research cruise NA090 using a Knudsen 3260 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435214
title: 数据描述.xlsx

description: this data set with simple description is free
DOI: 10.6084/m9.figshare.7435214.v1
title: 数据描述.xlsx

description: this data set with simple description is free
DOI: 10.7284/135241
title: SSV (Sound Speed Velocimeter) data collected during research cruise NA090 using a AML SV Xchange instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/135238
title: Expendable Probe data collected during research cruise NA091 using a Sippican MK21 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/135236
title: INS (Inertial Navigation System) data collected during research cruise NA091 using a Kongsberg Seatex MRU-5 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435157
title: Additional file 8: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S6. DESeq normalized RNASeq data representing the Klebsiella pneumoniae 342 genome in the in vitro biofilm model system across different pH stages. Average DESeq values are represented for all pH stages. (XLS 893 kb)
DOI: 10.6084/m9.figshare.7435160
title: Additional file 9: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S7. Sequence reads before and after quality filtering, and mapping results for all metagenome (MG) and metatranscriptome (MT) libraries. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7435157.v1
title: Additional file 8: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S6. DESeq normalized RNASeq data representing the Klebsiella pneumoniae 342 genome in the in vitro biofilm model system across different pH stages. Average DESeq values are represented for all pH stages. (XLS 893 kb)
DOI: 10.7284/135239
title: INS (Inertial Navigation System) data collected during research cruise NA091 using a Kongsberg Seapath 330+ instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435160.v1
title: Additional file 9: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S7. Sequence reads before and after quality filtering, and mapping results for all metagenome (MG) and metatranscriptome (MT) libraries. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7435148
title: Additional file 5: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S3. DESeq normalized RNASeq data representing eight different Veillonella genomes in the in vitro biofilm model system across different pH stages. Average DESeq values are represented for all pH stages. (XLS 3776 kb)
DOI: 10.6084/m9.figshare.7435151
title: Additional file 6: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S4. DESeq normalized RNASeq data representing the Streptococcus infantis X SEQF2216 genome in the in vitro biofilm model system across different pH stages. Average DESeq values are represented for all pH stages. (XLS 575 kb)
DOI: 10.6084/m9.figshare.7435154
title: Additional file 7: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S5. DESeq normalized RNASeq data representing the Granulicatella adiacens ATCC 49175 genome in the in vitro biofilm model system across different pH stages. Average DESeq values are represented for all pH stages. (XLS 605 kb)
DOI: 10.6084/m9.figshare.7435151.v1
title: Additional file 6: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S4. DESeq normalized RNASeq data representing the Streptococcus infantis X SEQF2216 genome in the in vitro biofilm model system across different pH stages. Average DESeq values are represented for all pH stages. (XLS 575 kb)
DOI: 10.6084/m9.figshare.7435154.v1
title: Additional file 7: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S5. DESeq normalized RNASeq data representing the Granulicatella adiacens ATCC 49175 genome in the in vitro biofilm model system across different pH stages. Average DESeq values are represented for all pH stages. (XLS 605 kb)
DOI: 10.7284/135240
title: Meteorological Station data collected during research cruise NA091 using a Coastal Weatherpak-2000 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435142
title: Additional file 3: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S1. DESeq normalized RNASeq data representing the Lactobacillus fermentum IFO 3956 genome in the in vitro biofilm model system across different pH stages. Average DESeq values are represented for all pH stages. (XLS 473 kb)
DOI: 10.6084/m9.figshare.7435145
title: Additional file 4: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S2. DESeq normalized RNASeq data representing expressed Streptococcus parasangunis ATCC15912 genes. Average DESeq values are represented for all pH stages. (XLS 1186 kb)
DOI: 10.6084/m9.figshare.7435148.v1
title: Additional file 5: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S3. DESeq normalized RNASeq data representing eight different Veillonella genomes in the in vitro biofilm model system across different pH stages. Average DESeq values are represented for all pH stages. (XLS 3776 kb)
DOI: 10.6084/m9.figshare.7435142.v1
title: Additional file 3: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S1. DESeq normalized RNASeq data representing the Lactobacillus fermentum IFO 3956 genome in the in vitro biofilm model system across different pH stages. Average DESeq values are represented for all pH stages. (XLS 473 kb)
DOI: 10.6084/m9.figshare.7435145.v1
title: Additional file 4: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S2. DESeq normalized RNASeq data representing expressed Streptococcus parasangunis ATCC15912 genes. Average DESeq values are represented for all pH stages. (XLS 1186 kb)
DOI: 10.7284/136026
title: Multibeam Echosounder data collected during research cruise NA091 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435133
title: Additional file 19: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S16. DESeq calculations showing differential gene expression of annotated open reading frames (ORFs) between time points and pH stages. Genes that were significantly changing in expression (fdr corrected p-value
DOI: 10.7284/136027
title: Multibeam Echosounder data collected during research cruise NA091 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435133.v1
title: Additional file 19: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S16. DESeq calculations showing differential gene expression of annotated open reading frames (ORFs) between time points and pH stages. Genes that were significantly changing in expression (fdr corrected p-value
DOI: 10.6084/m9.figshare.7435121
title: Additional file 15: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S13. DESeq normalized RNASeq data representing expressed genes associated with ammonia production and pH neutralization. (XLSX 123 kb)