cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3490613.v5
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: scripts]

description: This repository contains the shell, R and python scripts used to generate 4 different analyses:<br>Pre-processing: scripts responsible for generating of alignment files for downstream analyses, merging of said alignment files, generating of bigWig files for data visualisation and various Quality Control (QC)<br>Differential histone post-translational modifications (DHPTMs): scripts which estimate shift sizes and peaks from ChIP-seq data, and identify DHPTMs in peaks, transcription start site (TSS) regions and gene bodies<br>Differentially methylated regions (DMRs): scripts which identify DMRs within MeDIP-seq data<br>Differentially expressed genes (DEGs) and exons (DEEs): scripts responsible for counting number of reads in genes and exons, and determining DEGs and DEEs<br><br>The complete details on how to run the various scripts are included in the file run_scientific_data_analysis.pdf, which shows how to run all analyses with the aid of reference files (https://dx.doi.org/10.6084/m9.figshare.3487679) and demo samples (https://dx.doi.org/10.6084/m9.figshare.3487391)<br>
DOI: 10.6084/m9.figshare.3490613.v6
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: scripts]

description: This repository contains the shell, R and python scripts used to generate 4 different analyses:<br>Pre-processing: scripts responsible for generating of alignment files for downstream analyses, merging of said alignment files, generating of bigWig files for data visualisation and various Quality Control (QC)<br>Differential histone post-translational modifications (DHPTMs): scripts which estimate shift sizes and peaks from ChIP-seq data, and identify DHPTMs in peaks, transcription start site (TSS) regions and gene bodies<br>Differentially methylated regions (DMRs): scripts which identify DMRs within MeDIP-seq data<br>Differentially expressed genes (DEGs) and exons (DEEs): scripts responsible for counting number of reads in genes and exons, and determining DEGs and DEEs<br><br>The complete details on how to run the various scripts are included in the file run_scientific_data_analysis.pdf, which shows how to run all analyses with the aid of reference files (https://dx.doi.org/10.6084/m9.figshare.3487679) and demo samples (https://dx.doi.org/10.6084/m9.figshare.3487391)<br>
DOI: 10.6084/m9.figshare.3490613.v7
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: scripts]

description: This repository contains the shell, R and python scripts used to generate 4 different analyses:<br>Pre-processing: scripts responsible for generating of alignment files for downstream analyses, merging of said alignment files, generating of bigWig files for data visualisation and various Quality Control (QC)<br>Differential histone post-translational modifications (DHPTMs): scripts which estimate shift sizes and peaks from ChIP-seq data, and identify DHPTMs in peaks, transcription start site (TSS) regions and gene bodies<br>Differentially methylated regions (DMRs): scripts which identify DMRs within MeDIP-seq data<br>Differentially expressed genes (DEGs) and exons (DEEs): scripts responsible for counting number of reads in genes and exons, and determining DEGs and DEEs<br><br>The complete details on how to run the various scripts are included in the file run_scientific_data_analysis.pdf, which shows how to run all analyses with the aid of reference files (https://dx.doi.org/10.6084/m9.figshare.3487679) and demo samples (https://dx.doi.org/10.6084/m9.figshare.3487391)<br>
DOI: 10.6084/m9.figshare.3490592
title: Davis-Stober, Park, Brown and Regenwetter Supplementary Materials

description: ZIP file containing the Matlab code, data and a guide for recreating the analysis and figures from Davis-Stober, Park, Brown and Regenwetter (PNAS, 2016).
DOI: 10.6084/m9.figshare.3490592.v1
title: Davis-Stober, Park, Brown and Regenwetter Supplementary Materials

description: ZIP file containing the Matlab code, data and a guide for recreating the analysis and figures from Davis-Stober, Park, Brown and Regenwetter (PNAS, 2016).
DOI: 10.6084/m9.figshare.3490541
title: Subduction-related Late Cretaceous high-K volcanism in the Central Pontides orogenic belt: constraints on geodynamic implications

description: Mineral chemistry, major and trace elements, <sup>40</sup>Ar/<sup>39</sup>Ar age and Sr–Nd–Pb isotopic data are presented for the Late Cretaceous Hamsilos volcanic rocks in the Central Pontides, Turkey. The Hamsilos volcanic rocks mainly consist of basalt, andesite and associated pyroclastics (volcanic breccia, vitric tuff and crystal tuff). They display shoshonitic and high-K calc-alkaline affinities. The shoshonitic rocks contain plagioclase, clinopyroxene, alkali feldspar, phlogopite, analcime, sanidine, olivine, apatite and titanomagnetite, whereas the high-K calc-alkaline rocks contain plagioclase, clinopyroxene, orthopyroxene, magnetite / titanomagnetite in microgranular porphyritic, hyalo-microlitic porphyritic and glomeroporphyritic matrix. Mineral chemistry data reveal that the pressure condition of the clinopyroxene crystallisation for the shoshonitic rocks are between 1.4 and 6.3 kbar corresponds to 6–18-km depth and the high-K calc-alkaline rocks are between 5 and 12 km. <sup>40</sup>Ar/<sup>39</sup>Ar age data changing between 72 ± .5 Ma and 79.0 ± .3 Ma (Campanian) were determined for the Late Cretaceous Hamsilos volcanic rocks, contemporaneous with the subduction of the Neo-Tethyan Ocean beneath the Pontides. The studied volcanic rocks were enriched in the large-ion lithophile and light rare earth element contents, with pronounced depletion in the contents of high-field-strength elements. Chondrite-normalised rare earth element patterns (La<sub>N</sub>/Lu<sub>N</sub> = 6–17) show low to medium enrichment, indicating similar sources of the rock suite. Initial <sup>87</sup>Sr/<sup>86</sup>Sr values vary between .70615 and .70796, whereas initial <sup>143</sup>Nd/<sup>144</sup>Nd values change between .51228 and .51249. Initial <sup>206</sup>Pb/<sup>204</sup>Pb values vary between 18.001 and 18.349, <sup>207</sup>Pb/<sup>204</sup>Pb values between 15.611 and 15.629 and <sup>208</sup>Pb/<sup>204</sup>Pb values between 37.839 and 38.427. The main solidification processes involved in the evolution of the volcanic rocks consist of fractional crystallisation, with minor amounts of crustal contamination ± magma mixing. According to geochemical evidence, the shoshonitic melts in the Hamsilos volcanic rocks were possibly derived from the low degree of partial melting of a subcontinental lithospheric mantle (SCLM), while the high-K calc-alkaline melts were derived from relatively high degree of partial melting of SCLM that was enriched by fluids and/or sediments from a subduction of oceanic crust.
DOI: 10.6084/m9.figshare.3490541.v1
title: Subduction-related Late Cretaceous high-K volcanism in the Central Pontides orogenic belt: constraints on geodynamic implications

description: Mineral chemistry, major and trace elements, <sup>40</sup>Ar/<sup>39</sup>Ar age and Sr–Nd–Pb isotopic data are presented for the Late Cretaceous Hamsilos volcanic rocks in the Central Pontides, Turkey. The Hamsilos volcanic rocks mainly consist of basalt, andesite and associated pyroclastics (volcanic breccia, vitric tuff and crystal tuff). They display shoshonitic and high-K calc-alkaline affinities. The shoshonitic rocks contain plagioclase, clinopyroxene, alkali feldspar, phlogopite, analcime, sanidine, olivine, apatite and titanomagnetite, whereas the high-K calc-alkaline rocks contain plagioclase, clinopyroxene, orthopyroxene, magnetite / titanomagnetite in microgranular porphyritic, hyalo-microlitic porphyritic and glomeroporphyritic matrix. Mineral chemistry data reveal that the pressure condition of the clinopyroxene crystallisation for the shoshonitic rocks are between 1.4 and 6.3 kbar corresponds to 6–18-km depth and the high-K calc-alkaline rocks are between 5 and 12 km. <sup>40</sup>Ar/<sup>39</sup>Ar age data changing between 72 ± .5 Ma and 79.0 ± .3 Ma (Campanian) were determined for the Late Cretaceous Hamsilos volcanic rocks, contemporaneous with the subduction of the Neo-Tethyan Ocean beneath the Pontides. The studied volcanic rocks were enriched in the large-ion lithophile and light rare earth element contents, with pronounced depletion in the contents of high-field-strength elements. Chondrite-normalised rare earth element patterns (La<sub>N</sub>/Lu<sub>N</sub> = 6–17) show low to medium enrichment, indicating similar sources of the rock suite. Initial <sup>87</sup>Sr/<sup>86</sup>Sr values vary between .70615 and .70796, whereas initial <sup>143</sup>Nd/<sup>144</sup>Nd values change between .51228 and .51249. Initial <sup>206</sup>Pb/<sup>204</sup>Pb values vary between 18.001 and 18.349, <sup>207</sup>Pb/<sup>204</sup>Pb values between 15.611 and 15.629 and <sup>208</sup>Pb/<sup>204</sup>Pb values between 37.839 and 38.427. The main solidification processes involved in the evolution of the volcanic rocks consist of fractional crystallisation, with minor amounts of crustal contamination ± magma mixing. According to geochemical evidence, the shoshonitic melts in the Hamsilos volcanic rocks were possibly derived from the low degree of partial melting of a subcontinental lithospheric mantle (SCLM), while the high-K calc-alkaline melts were derived from relatively high degree of partial melting of SCLM that was enriched by fluids and/or sediments from a subduction of oceanic crust.
DOI: 10.6084/m9.figshare.3490523
title: Lista Espécies de Itaúnas.pdf

description: Lista de Espécies de Angiospermas do Parque Estadual de Itaúnas, ES, Brasil
DOI: 10.6084/m9.figshare.3490406
title: Spatial variations in larch needle and soil δ<sup>15</sup>N at a forest–grassland boundary in northern Mongolia

description: The spatial patterns of plant and soil δ<sup>15</sup>N and associated processes in the N cycle were investigated at a forest–grassland boundary in northern Mongolia. Needles of <i>Larix sibirica</i> Ledeb. and soils collected from two study areas were analysed to calculate the differences in δ<sup>15</sup>N between needle and soil (Δδ<sup>15</sup>N). Δδ<sup>15</sup>N showed a clear variation, ranging from −8 ‰ in the forest to −2 ‰ in the grassland boundary, and corresponded to the accumulation of organic layer. In the forest, the separation of available N produced in the soil with <sup>15</sup>N-depleted N uptake by larch and <sup>15</sup>N-enriched N immobilization by microorganisms was proposed to cause large Δδ<sup>15</sup>N, whereas in the grassland boundary, small Δδ<sup>15</sup>N was explained by the transport of the most available N into larch. The divergence of available N between larch and microorganisms in the soil, and the accumulation of diverged N in the organic layer control the variation in Δδ<sup>15</sup>N.
DOI: 10.6084/m9.figshare.3490406.v1
title: Spatial variations in larch needle and soil δ<sup>15</sup>N at a forest–grassland boundary in northern Mongolia

description: The spatial patterns of plant and soil δ<sup>15</sup>N and associated processes in the N cycle were investigated at a forest–grassland boundary in northern Mongolia. Needles of <i>Larix sibirica</i> Ledeb. and soils collected from two study areas were analysed to calculate the differences in δ<sup>15</sup>N between needle and soil (Δδ<sup>15</sup>N). Δδ<sup>15</sup>N showed a clear variation, ranging from −8 ‰ in the forest to −2 ‰ in the grassland boundary, and corresponded to the accumulation of organic layer. In the forest, the separation of available N produced in the soil with <sup>15</sup>N-depleted N uptake by larch and <sup>15</sup>N-enriched N immobilization by microorganisms was proposed to cause large Δδ<sup>15</sup>N, whereas in the grassland boundary, small Δδ<sup>15</sup>N was explained by the transport of the most available N into larch. The divergence of available N between larch and microorganisms in the soil, and the accumulation of diverged N in the organic layer control the variation in Δδ<sup>15</sup>N.
DOI: 10.6084/m9.figshare.3490400
title: Contribution of seedling vigour and anoxia/hypoxia-responsive genes to submergence tolerance in Vietnamese lowland rice (<i>Oryza sativa</i> L.)

description: A direct-seeded rice cultivation system has been widely adopted in Asian countries. Optimum germination and vigorous seedling growth under submergence are key traits for the practice of direct seeding. We studied the post-germination seedling vigour in Vietnamese lowland rice accessions based on three bio-parameters, shoot elongation growth under five-day submergence in water-filled test-tubes, seedling recovery rate five days after transferring submerged seedlings to pots with soil and seedling survival rate 21 days after sowing seeds in nursery beds and immediate incubation under submergence. A large diversity was found in seedling vigour thus estimated among the accessions. Significantly high correlations were observed among all three bio-parameters, verifying the contribution of seedling vigour to the manifestation of submergence tolerance at this critical stage of rice development. To examine the roles of anoxia/hypoxia-responsive genes, the expression of 17 candidate genes was studied by reverse transcription polymerase chain reaction (RT-PCR) and compared between selected vigorous and non-vigorous groups of accessions. Transcripts of all but two genes showed marked accumulation in submerged seedlings. No differences, however, were found between the two contrasting groups. The observed common and coordinate expression of anoxia/hypoxia-induced genes suggests that they might assume roles in attaining baseline tolerance against submergence stress. It was also suggested that some unknown genetic factors are operating in determining cultivar/genotype-specific levels of submergence tolerance as assessed by post-germination seedling vigour.
DOI: 10.6084/m9.figshare.3490400.v2
title: Contribution of seedling vigour and anoxia/hypoxia-responsive genes to submergence tolerance in Vietnamese lowland rice (<i>Oryza sativa</i> L.)

description: A direct-seeded rice cultivation system has been widely adopted in Asian countries. Optimum germination and vigorous seedling growth under submergence are key traits for the practice of direct seeding. We studied the post-germination seedling vigour in Vietnamese lowland rice accessions based on three bio-parameters, shoot elongation growth under five-day submergence in water-filled test-tubes, seedling recovery rate five days after transferring submerged seedlings to pots with soil and seedling survival rate 21 days after sowing seeds in nursery beds and immediate incubation under submergence. A large diversity was found in seedling vigour thus estimated among the accessions. Significantly high correlations were observed among all three bio-parameters, verifying the contribution of seedling vigour to the manifestation of submergence tolerance at this critical stage of rice development. To examine the roles of anoxia/hypoxia-responsive genes, the expression of 17 candidate genes was studied by reverse transcription polymerase chain reaction (RT-PCR) and compared between selected vigorous and non-vigorous groups of accessions. Transcripts of all but two genes showed marked accumulation in submerged seedlings. No differences, however, were found between the two contrasting groups. The observed common and coordinate expression of anoxia/hypoxia-induced genes suggests that they might assume roles in attaining baseline tolerance against submergence stress. It was also suggested that some unknown genetic factors are operating in determining cultivar/genotype-specific levels of submergence tolerance as assessed by post-germination seedling vigour.
DOI: 10.6084/m9.figshare.3490331
title: Evolution of the Proto-Tethys in the Baoshan block along the East Gondwana margin: constraints from early Palaeozoic magmatism

description: Zircon U–Pb ages and geochemical and isotopic data for Late Ordovician granites in the Baoshan Block reveal the early Palaeozoic tectonic evolution of the margin of East Gondwana. The granites are high-K, calc-alkaline, metaluminous to strongly peraluminous rocks with A/CNK values of 0.93–1.18, are enriched in SiO<sub>2</sub>, K<sub>2</sub>O, and Rb, and depleted in Nb, P, Ti, Eu, and heavy rare earth elements, which indicates the crystallization fractionation of the granitic magma. Zircon U–Pb dating indicates that they formed at ca. 445 Ma. High initial <sup>87</sup>Sr/<sup>86</sup>Sr ratios of 0.719761–0.726754, negative ɛ<sub>Nd</sub>(t) values of –6.6 to –8.3, and two-stage model ages of 1.52–1.64 Ga suggest a crustal origin, with the magmas derived from the partial melting of ancient metagreywacke at high temperature. A synthesis of data for the early Palaeozoic igneous rocks in the Baoshan Block and adjacent Tengchong Block indicates two stages of flare-up of granitic and mafic magmatism caused by different tectonic settings along the East Gondwana margin. Late Cambrian to Early Ordovician granitic rocks (ca. 490 Ma) were produced when underplated mafic magmas induced crustal melting along the margin of East Gondwana related to the break-off of subducted Proto-Tethyan oceanic slab. In addition, the cession of the mafic magmatism between late Cambrian-Early Ordovician and Late Ordovician could have been caused by the collision of the Baoshan Block and outward micro-continent along the margin of East Gondwana and crust and lithosphere thickening. The Late Ordovician granites in the Baoshan Block were produced in an extensional setting resulting from the delamination of an already thickened crust and lithospheric mantle followed by the injection of synchronous mafic magma.
DOI: 10.6084/m9.figshare.3490331.v1
title: Evolution of the Proto-Tethys in the Baoshan block along the East Gondwana margin: constraints from early Palaeozoic magmatism

description: Zircon U–Pb ages and geochemical and isotopic data for Late Ordovician granites in the Baoshan Block reveal the early Palaeozoic tectonic evolution of the margin of East Gondwana. The granites are high-K, calc-alkaline, metaluminous to strongly peraluminous rocks with A/CNK values of 0.93–1.18, are enriched in SiO<sub>2</sub>, K<sub>2</sub>O, and Rb, and depleted in Nb, P, Ti, Eu, and heavy rare earth elements, which indicates the crystallization fractionation of the granitic magma. Zircon U–Pb dating indicates that they formed at ca. 445 Ma. High initial <sup>87</sup>Sr/<sup>86</sup>Sr ratios of 0.719761–0.726754, negative ɛ<sub>Nd</sub>(t) values of –6.6 to –8.3, and two-stage model ages of 1.52–1.64 Ga suggest a crustal origin, with the magmas derived from the partial melting of ancient metagreywacke at high temperature. A synthesis of data for the early Palaeozoic igneous rocks in the Baoshan Block and adjacent Tengchong Block indicates two stages of flare-up of granitic and mafic magmatism caused by different tectonic settings along the East Gondwana margin. Late Cambrian to Early Ordovician granitic rocks (ca. 490 Ma) were produced when underplated mafic magmas induced crustal melting along the margin of East Gondwana related to the break-off of subducted Proto-Tethyan oceanic slab. In addition, the cession of the mafic magmatism between late Cambrian-Early Ordovician and Late Ordovician could have been caused by the collision of the Baoshan Block and outward micro-continent along the margin of East Gondwana and crust and lithosphere thickening. The Late Ordovician granites in the Baoshan Block were produced in an extensional setting resulting from the delamination of an already thickened crust and lithospheric mantle followed by the injection of synchronous mafic magma.
DOI: 10.6084/m9.figshare.3490325
title: The DNA methylome data generated using MeDIP-Seq technique from pig loin.

description: loin samples from four pairs of Duroc gilt littermates, with an average body weight of 101.6 ± 5.3 kg and average age of 184 ± 9 days, were collected from commercial breeding farms after slaughter.Genomic DNA was extracted from LDM samples and isolated using the phenol-chloroform-isoamyl alcohol method as follows: firstly, LDM tissue was frozen in liquid nitrogen, crushed with a mortar and pestle, and digested for 12 hr at 55 °C in a lysis buffer and 0.1 mg/ml of proteinase K. At the end of the incubation, 5 ml of protein PPT buffer was added to precipitate proteins without heating. After centrifugation of the solution at 13,000 rpm for 10 min, the supernatant was collected in a clean tube and 5 ml of phenol-chloroform-isoamyl alcohol (25:24:1) was added. After a further centrifugation at 13,000 rpm for 15 min, 5 ml of the aqueous phase was transferred to a clean tube, and the DNA was precipitated using 0.5 ml of 3 M sodium acetate and 10 ml of 100 % ethanol. The pellets were washed with 70 % ethanol, allowed to dry, and dissolved in TE buffer.For each sample, 1.2 μg of genomic DNA was randomly sheared to approximately 200–300 bp fragments using a Covaris S2. MeDIP libraries were constructed using the TruSeq DNA Sample Prep kit (Illumina, San Diego, CA, USA) following the manufacture’s recommended protocol. The DNA fragments were end-repaired, phosphorylated, poly(A)-tailed, and then ligated with Illumina single read adapters. The adapter-ligated DNA fragments sized approximately 250­–300 bp were screened by gel electrophoresis and purified with MinElute Gel Extraction kit (Qiagen, Valencia, CA, USA), and were used for MeDIP enrichment using Methylated DNA Immunoprecipitation kit (Diagenode, Liège, Belgium) following the manufacture’s recommendation. The immunoprecipitated DNA fragments were then PCR amplified: 98 °C for 30 sec; 10 cycles of 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec; and 72°C for 5 min. MeDIP libraries were quantified using Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen, Carlsbad, CA, USA). Flow cells were prepared with 8 pM DNA using the manufacture’s recommended protocol and sequenced on an Illumina Genome Analyzer II to generate single-end 36 bp reads.
DOI: 10.5517/ccdc.csd.cc1zdsz4
title: CCDC 1829557: Experimental Crystal Structure Determination

description: Related Article: Namrim Heo, Ilyong Jung, Dae Kyum Kim, Sang Hoon Han, Kooyeon Lee, Phil Ho Lee|2020|Org.Lett.|22|6562|doi:10.1021/acs.orglett.0c02333
description: Related Article: Phil Ho Lee|2019|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc1zkhyz
title: CCDC 1834082: Experimental Crystal Structure Determination

description: Related Article: Namrim Heo, Ilyong Jung, Dae Kyum Kim, Sang Hoon Han, Kooyeon Lee, Phil Ho Lee|2020|Org.Lett.|22|6562|doi:10.1021/acs.orglett.0c02333
description: Related Article: Phil Ho Lee|2019|CSD Communication|||