cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.15128094
title: Significantly different glycerolipid metabolites between horses fed silage and hay

description: The table provides information about differently regulated glycerolipid metabolites between horses fed silage and hay diet. <br><br><br><br>
DOI: 10.6084/m9.figshare.15128127
title: Additional file 3 of SDG712, a Putative H3K9-Specific Methyltransferase Encoding Gene, Delays Flowering through Repressing the Expression of Florigen Genes in Rice

description: Additional file 3: Supplemental Table 2. Primers used for vector construction and gene expression analysis.
DOI: 10.6084/m9.figshare.15128124.v1
title: Additional file 2 of SDG712, a Putative H3K9-Specific Methyltransferase Encoding Gene, Delays Flowering through Repressing the Expression of Florigen Genes in Rice

description: Additional file 2: Supplemental Table 1. Global gene expressions in wild-type rice and hd1–3 mutant.
DOI: 10.6084/m9.figshare.15128127.v1
title: Additional file 3 of SDG712, a Putative H3K9-Specific Methyltransferase Encoding Gene, Delays Flowering through Repressing the Expression of Florigen Genes in Rice

description: Additional file 3: Supplemental Table 2. Primers used for vector construction and gene expression analysis.
DOI: 10.6084/m9.figshare.15128124
title: Additional file 2 of SDG712, a Putative H3K9-Specific Methyltransferase Encoding Gene, Delays Flowering through Repressing the Expression of Florigen Genes in Rice

description: Additional file 2: Supplemental Table 1. Global gene expressions in wild-type rice and hd1–3 mutant.
DOI: 10.5281/zenodo.10721076
title: Scripts and metadata for paper ECS22-0498 "Long-distance post-release movements challenge the metapopulation restoration of bearded vultures"

description: Codes and metadata for accepted paper: 

ECS22-0498

TréhinC., Duriez O., Sarrazin F., Betton B., Fonderflick J., Loercher F., Marlé E, Seguin J-F., Traversier J., Ziletti N., Mihoub J-B., Long-distance post-release movements challenge the metapopulation restoration of bearded vultures, Ecosphere (accepted)
DOI: 10.5281/zenodo.10721077
title: Scripts and metadata for paper ECS22-0498 "Long-distance post-release movements challenge the metapopulation restoration of bearded vultures"

description: Codes and metadata for accepted paper: 

ECS22-0498

TréhinC., Duriez O., Sarrazin F., Betton B., Fonderflick J., Loercher F., Marlé E, Seguin J-F., Traversier J., Ziletti N., Mihoub J-B., Long-distance post-release movements challenge the metapopulation restoration of bearded vultures, Ecosphere (accepted)
DOI: 10.6084/m9.figshare.6739565
title: Additional file 2: of PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia

description: PathCORE-T network constructed from a Pseudomonas aeruginosa compendium using 10 eADAGE models analyzed with KEGG pathway annotations. (TSV 16 kb)
DOI: 10.6084/m9.figshare.6739565.v1
title: Additional file 2: of PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia

description: PathCORE-T network constructed from a Pseudomonas aeruginosa compendium using 10 eADAGE models analyzed with KEGG pathway annotations. (TSV 16 kb)
DOI: 10.6084/m9.figshare.8312435
title: Circular RNA <i>circHIPK3</i> modulates autophagy via <i>MIR124-3p</i>-STAT3-PRKAA/AMPKα signaling in STK11 mutant lung cancer

description: The role of circular RNA in cancer is emerging. A newly reported circular RNA <i>HIPK3</i> (<i>circHIPK3)</i> is critical in cell proliferation of various cancer types, although its role in non-small cell lung cancer (NSCLC), has yet to be elucidated. Our results provided evidence that silencing of <i>circHIPK3</i> significantly impaired cell proliferation, migration, invasion and induced macroautophagy/autophagy. Mechanistically, we uncovered that autophagy was induced upon loss of <i>circHIPK3</i> via the <i>MIR124-3p</i>-STAT3-PRKAA/AMPKa axis in STK11 mutant lung cancer cell lines (A549 and H838). STAT3 abrogation as well as transfection with a <i>MIR124-3p</i> mimic, recapitulated the induction of autophagy. We also demonstrated antagonistic regulation on autophagy between <i>circHIPK3</i> and linear <i>HIPK3</i> (<i>linHIPK3</i>). We therefore propose that the ratio between <i>circHIPK3</i> and <i>linHIPK3</i> (C:L ratio) may reflect autophagy levels in cancer cells. We observed that a high C:L ratio (&gt;0.49) was an indicator of poor survival, especially in advanced-stage NSCLC patients. These results support that <i>circHIPK3</i> is a key autophagy regulator in a subset of lung cancer and has potential clinical use as a prognostic factor. The circular RNA <i>HIPK3</i> (<i>circHIPK3)</i> functions as an oncogene and autophagy regulator may potential use as a prognostic marker and therapeutic target in lung cancer. <b>Abbreviations</b> 3-MA: 3-methyladenine; AMPK: AMP-activated protein kinase; ATG7: autophagy related 7; Baf-A: bafilomycin A<sub>1</sub>; BECN1: beclin 1; <i>circHIPK3</i>: circular HIPK3; CQ: chloroquine; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; HIPK3: homeodomain interacting protein kinase 3; IL6R: interleukin 6 receptor; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; NSCLC: non-small cell lung cancer; RFP: red fluorescent protein; RPS6KB1/S6K: ribosomal protein S6 kinase B1; SQSTM1/p62: sequestosome 1; STAT3: signal transducer and activator of transcription 3; STK11: serine/threonine kinase 11
DOI: 10.6084/m9.figshare.8312435.v2
title: Circular RNA <i>circHIPK3</i> modulates autophagy via <i>MIR124-3p</i>-STAT3-PRKAA/AMPKα signaling in STK11 mutant lung cancer

description: The role of circular RNA in cancer is emerging. A newly reported circular RNA <i>HIPK3</i> (<i>circHIPK3)</i> is critical in cell proliferation of various cancer types, although its role in non-small cell lung cancer (NSCLC), has yet to be elucidated. Our results provided evidence that silencing of <i>circHIPK3</i> significantly impaired cell proliferation, migration, invasion and induced macroautophagy/autophagy. Mechanistically, we uncovered that autophagy was induced upon loss of <i>circHIPK3</i> via the <i>MIR124-3p</i>-STAT3-PRKAA/AMPKa axis in STK11 mutant lung cancer cell lines (A549 and H838). STAT3 abrogation as well as transfection with a <i>MIR124-3p</i> mimic, recapitulated the induction of autophagy. We also demonstrated antagonistic regulation on autophagy between <i>circHIPK3</i> and linear <i>HIPK3</i> (<i>linHIPK3</i>). We therefore propose that the ratio between <i>circHIPK3</i> and <i>linHIPK3</i> (C:L ratio) may reflect autophagy levels in cancer cells. We observed that a high C:L ratio (&gt;0.49) was an indicator of poor survival, especially in advanced-stage NSCLC patients. These results support that <i>circHIPK3</i> is a key autophagy regulator in a subset of lung cancer and has potential clinical use as a prognostic factor. The circular RNA <i>HIPK3</i> (<i>circHIPK3)</i> functions as an oncogene and autophagy regulator may potential use as a prognostic marker and therapeutic target in lung cancer. <b>Abbreviations</b> 3-MA: 3-methyladenine; AMPK: AMP-activated protein kinase; ATG7: autophagy related 7; Baf-A: bafilomycin A<sub>1</sub>; BECN1: beclin 1; <i>circHIPK3</i>: circular HIPK3; CQ: chloroquine; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; HIPK3: homeodomain interacting protein kinase 3; IL6R: interleukin 6 receptor; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; NSCLC: non-small cell lung cancer; RFP: red fluorescent protein; RPS6KB1/S6K: ribosomal protein S6 kinase B1; SQSTM1/p62: sequestosome 1; STAT3: signal transducer and activator of transcription 3; STK11: serine/threonine kinase 11
DOI: 10.6084/m9.figshare.8312435.v1
title: Circular RNA <i>circHIPK3</i> modulates autophagy via <i>MIR124-3p</i>-STAT3-PRKAA/AMPKα signaling in STK11 mutant lung cancer

description: The role of circular RNA in cancer is emerging. A newly reported circular RNA <i>HIPK3</i> (<i>circHIPK3)</i> is critical in cell proliferation of various cancer types, although its role in non-small cell lung cancer (NSCLC), has yet to be elucidated. Our results provided evidence that silencing of <i>circHIPK3</i> significantly impaired cell proliferation, migration, invasion and induced macroautophagy/autophagy. Mechanistically, we uncovered that autophagy was induced upon loss of <i>circHIPK3</i> via the <i>MIR124-3p</i>-STAT3-PRKAA/AMPKa axis in STK11 mutant lung cancer cell lines (A549 and H838). STAT3 abrogation as well as transfection with a <i>MIR124-3p</i> mimic, recapitulated the induction of autophagy. We also demonstrated antagonistic regulation on autophagy between <i>circHIPK3</i> and linear <i>HIPK3</i> (<i>linHIPK3</i>). We therefore propose that the ratio between <i>circHIPK3</i> and <i>linHIPK3</i> (C:L ratio) may reflect autophagy levels in cancer cells. We observed that a high C:L ratio (&gt;0.49) was an indicator of poor survival, especially in advanced-stage NSCLC patients. These results support that <i>circHIPK3</i> is a key autophagy regulator in a subset of lung cancer and has potential clinical use as a prognostic factor. The circular RNA <i>HIPK3</i> (<i>circHIPK3)</i> functions as an oncogene and autophagy regulator may potential use as a prognostic marker and therapeutic target in lung cancer. <b>Abbreviations</b> 3-MA: 3-methyladenine; AMPK: AMP-activated protein kinase; ATG7: autophagy related 7; Baf-A: bafilomycin A<sub>1</sub>; BECN1: beclin 1; <i>circHIPK3</i>: circular HIPK3; CQ: chloroquine; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; HIPK3: homeodomain interacting protein kinase 3; IL6R: interleukin 6 receptor; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; NSCLC: non-small cell lung cancer; RFP: red fluorescent protein; RPS6KB1/S6K: ribosomal protein S6 kinase B1; SQSTM1/p62: sequestosome 1; STAT3: signal transducer and activator of transcription 3; STK11: serine/threonine kinase 11
DOI: 10.6084/m9.figshare.6739592
title: Additional file 3: of PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia

description: PathCORE-T network constructed from TCGA data using NMF models analyzed with PID pathway annotations.Â  (TSV 5 kb)
DOI: 10.6084/m9.figshare.6739592.v1
title: Additional file 3: of PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia

description: PathCORE-T network constructed from TCGA data using NMF models analyzed with PID pathway annotations.Â  (TSV 5 kb)
DOI: 10.25935/m643-rz62
title: Bursts of Auroral Kilometric Radiation individually selected from Wind/WAVES data (1995-1999)

description: This event list contains start and end times for automatically detected bursts of Auroral Kilometric Radiation (AKR), extracted from Wind/WAVES data. Also provided are the upper and lower frequency limits as a function of time within the burst. This dataset covers the years 1995 to 1999.
DOI: 10.5281/zenodo.10717483
title: Data (part 2) from Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models

description: Part 2 contains:



longest_isoforms_gopredsim_seqvec_F_to_O.tar.gz : GOPredSim GO annotation using SeqVec model for the longest isoform or species whose code first letter goes from F to O.

IC_longest_isoforms_gopredsim_prott5.tar.gz : Information content (IC) of the unfiltered GOPredSim-ProtT5 GO annotation of the longest isoforms of all species.

IC_longest_isoforms_gopredsim_seqvec.tar.gz : IC of the unfiltered GOPredSim-SeqVec GO annotation of the longest isoforms of all species.

IC_all_isoforms_eggnog_filtered_go_terms_cdhit.tar.gz : IC of the eggNOG-mapper GO annotation of all isoforms of a subset of 102 species. Isoforms removed by CD-HIT are filtered from this file (but included in the original eggNOG-mapper output).

IC_all_isoforms_gopredsim_prott5.tar.gz : IC of the GOPredSim-ProtT5 GO annotation of all isoforms of a subset of 102 species.

IC_all_isoforms_gopredsim_seqvec.tar.gz : IC of the GOPredSim-SeqVec GO annotation of all isoforms of a subset of 102 species.
DOI: 10.5281/zenodo.10717484
title: Data (part 2) from Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models

description: Part 2 contains:



longest_isoforms_gopredsim_seqvec_F_to_O.tar.gz : GOPredSim GO annotation using SeqVec model for the longest isoform or species whose code first letter goes from F to O.

IC_longest_isoforms_gopredsim_prott5.tar.gz : Information content (IC) of the unfiltered GOPredSim-ProtT5 GO annotation of the longest isoforms of all species.

IC_longest_isoforms_gopredsim_seqvec.tar.gz : IC of the unfiltered GOPredSim-SeqVec GO annotation of the longest isoforms of all species.

IC_all_isoforms_eggnog_filtered_go_terms_cdhit.tar.gz : IC of the eggNOG-mapper GO annotation of all isoforms of a subset of 102 species. Isoforms removed by CD-HIT are filtered from this file (but included in the original eggNOG-mapper output).

IC_all_isoforms_gopredsim_prott5.tar.gz : IC of the GOPredSim-ProtT5 GO annotation of all isoforms of a subset of 102 species.

IC_all_isoforms_gopredsim_seqvec.tar.gz : IC of the GOPredSim-SeqVec GO annotation of all isoforms of a subset of 102 species.
DOI: 10.6084/m9.figshare.25304209
title: <b>Study of Accessory Gene Regulator, Biofilm formation, and Antibiotics Resistance in </b><b><i>Staphylococcus aureus</i></b><b> Isolated from Pediatric Patients with Health Care associated Sepsis</b>

description: <b>Study of Accessory Gene Regulator, Biofilm formation, and Antibiotics Resistance in </b><b><i>Staphylococcus aureus</i></b><b> Isolated from Pediatric Patients with Health Care associated Sepsis</b>
DOI: 10.6084/m9.figshare.25304209.v1
title: <b>Study of Accessory Gene Regulator, Biofilm formation, and Antibiotics Resistance in </b><b><i>Staphylococcus aureus</i></b><b> Isolated from Pediatric Patients with Health Care associated Sepsis</b>

description: <b>Study of Accessory Gene Regulator, Biofilm formation, and Antibiotics Resistance in </b><b><i>Staphylococcus aureus</i></b><b> Isolated from Pediatric Patients with Health Care associated Sepsis</b>
DOI: 10.5281/zenodo.10717773
title: Data (part 3) from Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models

description: Part 3 contains:



longest_isoforms_gopredsim_seqvec_P_to_Z.tar.gz : GOPredSim GO annotation using SeqVec model for the longest isoform or species whose code first letter goes from P to Z.
DOI: 10.5281/zenodo.10717774
title: Data (part 3) from Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models

description: Part 3 contains:



longest_isoforms_gopredsim_seqvec_P_to_Z.tar.gz : GOPredSim GO annotation using SeqVec model for the longest isoform or species whose code first letter goes from P to Z.
DOI: 10.5281/zenodo.10717782
title: Data (part 4) from Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models

description: Part 4 contains:



all_isoforms_gopredsim.tar.gz : GOPredSim (ProtT5 and SeqVec) GO annotation for all isoforms for a subset of 102 species.

IC_longest_isoforms_deepgoplus.tar.gz : Information content (IC) of the unfiltered DeepGOPlus GO annotation of the longest isoforms of all species.
DOI: 10.5281/zenodo.10717783
title: Data (part 4) from Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models

description: Part 4 contains:



all_isoforms_gopredsim.tar.gz : GOPredSim (ProtT5 and SeqVec) GO annotation for all isoforms for a subset of 102 species.

IC_longest_isoforms_deepgoplus.tar.gz : Information content (IC) of the unfiltered DeepGOPlus GO annotation of the longest isoforms of all species.
DOI: 10.5281/zenodo.10717884
title: Data (part 5) from Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models

description: Part 5 contains:



IC_longest_isoforms_eggnog_filtered_goterms_cdhit.tar.gz : Information content (IC) of the eggNOG-mapper GO annotation of the longest isoforms of all species (proteins filtered by CD-HIT removed).
DOI: 10.5281/zenodo.10717885
title: Data (part 5) from Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models

description: Part 5 contains:



IC_longest_isoforms_eggnog_filtered_goterms_cdhit.tar.gz : Information content (IC) of the eggNOG-mapper GO annotation of the longest isoforms of all species (proteins filtered by CD-HIT removed).
DOI: 10.5281/zenodo.10717909
title: Data (part 6) from Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models

description: Part 6 contains:



model_organisms_semsim_go_cats.txt : semantic similarity separated by GO category between the GO annotations from GOPredSim-ProtT5 before and after removing a given model organism from the lookup dataset.

model_organisms_removed_confidence_min.txt : minimum reliability index ("confidence") per gene of GO annotations from GOPredSim-ProtT5 after removing a given model organism from the lookup dataset.

model_organisms_prott5.tar.gz : GO annotations from GOPredSim-ProtT5 after removing a given model organism from the lookup dataset.

model_organisms_orig_confidence_min.txt : minimum reliability index ("confidence") per gene of GO annotations from GOPredSim-ProtT5 before removing a given model organism from the lookup dataset.

all_isoforms_cdhit_clustr.tar.gz : CD-HIT clusters results for all isoforms for a subset of 102 species.

all_isoforms_larger_5k.tar.gz : headers of sequences that are more than 5000 aminoacids long after CD-HIT for all isoforms of a subset of 102 species.

longest_cdhit_clustr.tar.gz : CD-HIT clusters results for the longest isoforms of all species.

longest_larger_5k.tar.gz : headers of sequences that are more than 5000 aminoacids long after CD-HIT for the longest isoforms all species.
DOI: 10.5281/zenodo.10717910
title: Data (part 6) from Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models

description: Part 6 contains:



model_organisms_semsim_go_cats.txt : semantic similarity separated by GO category between the GO annotations from GOPredSim-ProtT5 before and after removing a given model organism from the lookup dataset.

model_organisms_removed_confidence_min.txt : minimum reliability index ("confidence") per gene of GO annotations from GOPredSim-ProtT5 after removing a given model organism from the lookup dataset.

model_organisms_prott5.tar.gz : GO annotations from GOPredSim-ProtT5 after removing a given model organism from the lookup dataset.

model_organisms_orig_confidence_min.txt : minimum reliability index ("confidence") per gene of GO annotations from GOPredSim-ProtT5 before removing a given model organism from the lookup dataset.

all_isoforms_cdhit_clustr.tar.gz : CD-HIT clusters results for all isoforms for a subset of 102 species.

all_isoforms_larger_5k.tar.gz : headers of sequences that are more than 5000 aminoacids long after CD-HIT for all isoforms of a subset of 102 species.

longest_cdhit_clustr.tar.gz : CD-HIT clusters results for the longest isoforms of all species.

longest_larger_5k.tar.gz : headers of sequences that are more than 5000 aminoacids long after CD-HIT for the longest isoforms all species.
DOI: 10.25935/hfjx-xx26
title: Bursts of Auroral Kilometric Radiation individually selected from Wind/WAVES data (2000-2004)

description: This event list contains start and end times for automatically detected bursts of Auroral Kilometric Radiation (AKR), extracted from Wind/WAVES data. Also provided are the upper and lower frequency limits as a function of time within the burst. This dataset covers the years 2000 to 2004.
DOI: 10.6084/m9.figshare.15128246
title: Additional file 4 of JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen

description: Additional file 4: Table S3. Summary of transcriptome sequencing data.
DOI: 10.6084/m9.figshare.15128246.v1
title: Additional file 4 of JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen

description: Additional file 4: Table S3. Summary of transcriptome sequencing data.
DOI: 10.6084/m9.figshare.15128252
title: Additional file 5 of JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen

description: Additional file 5: Table S4. Summary of mapped reads in transcriptome sequencing.
DOI: 10.6084/m9.figshare.15128252.v1
title: Additional file 5 of JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen

description: Additional file 5: Table S4. Summary of mapped reads in transcriptome sequencing.
DOI: 10.6084/m9.figshare.15128255
title: Additional file 6 of JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen

description: Additional file 6: Table S5. Summary of differentially expressed genes in transcriptome analysis.
DOI: 10.6084/m9.figshare.15128255.v1
title: Additional file 6 of JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen

description: Additional file 6: Table S5. Summary of differentially expressed genes in transcriptome analysis.
DOI: 10.6084/m9.figshare.15128258
title: Additional file 7 of JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen

description: Additional file 7: Table S6. Expression data of JA signaling pathway genes after MeJA and S. delphinii treatment in D. catenatum.
DOI: 10.6084/m9.figshare.15128258.v1
title: Additional file 7 of JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen

description: Additional file 7: Table S6. Expression data of JA signaling pathway genes after MeJA and S. delphinii treatment in D. catenatum.
DOI: 10.6084/m9.figshare.15128267
title: Additional file 9 of JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen

description: Additional file 9: Table S7. Primers used for RT-qPCR.
DOI: 10.6084/m9.figshare.15128267.v1
title: Additional file 9 of JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen

description: Additional file 9: Table S7. Primers used for RT-qPCR.
DOI: 10.6084/m9.figshare.15128286
title: Additional file 1 of Genome-wide identification of the MADS-box transcription factor family in autotetraploid cultivated alfalfa (Medicago sativa L.) and expression analysis under abiotic stress

description: Additional file 1: Table S1. List of the MADS-bBox sequences in Alfalfa. Table S2. Protein property of MsMADS-box proteins. Table S3. Gene ontology (GO) annotation results of 120 MsMADS-box genes. Table S4. The structural features of motif 1-20. Table S5. Expression (FPKM) of MsMADS-box genes in different tissues. Table S6. Expression (FPKM) of MsMADS-box genes in response to cold, ABA, drought, and salt treatment in alfalfa. Table S7. Ct values of eight MsMADS-box genes in response to cold, drought, salt, and ABA treatment in alfalfa. Table S8. Sequences of primers used in qRT-PCR.