cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1466929.v3
title: Rawdata_10

description: Genotyping data for landrace and cultivated lines from the National Small Grains Collection. The dataset has been devided in 11 parts. <strong>This is part 10. Make sure to download all 11 parts</strong>. Data used in the article: "Barley landraces are characterized by geographically heterogeneous genomic origins". Published in Genome Biology Use the following command to put the pieces together: % cat * &gt;./My_complete_data.txt The scripts used to analyze and plot the data are available in GitHub: https://github.com/AnaPoets/BarleyLandraces
DOI: 10.6084/m9.figshare.1466919
title: Rawdata_01 - Barley landraces are characterized by geographically heterogeneous genomic origins

description: Genotyping data for landrace and cultivated lines from the National Small Grains Collection. The dataset has been devided in 11 parts. <strong>This is part 01. Make sure to download all 11 parts.</strong> Data used in the article: "Barley landraces are characterized by geographically heterogeneous genomic origins". Published in Genome Biology Use the following command to put the pieces together: % cat * &gt;./My_complete_data.txt The scripts used to analyze and plot the data are available in GitHub: https://github.com/AnaPoets/BarleyLandraces
DOI: 10.6084/m9.figshare.1466920
title: Rawdata_02 - Barley landraces are characterized by geographically heterogeneous genomic origins

description: Genotyping data for landrace and cultivated lines from the National Small Grains Collection. The dataset has been devided in 11 parts. <strong>This is part 02. Make sure to download all 11 parts.</strong> Data used in the article: "Barley landraces are characterized by geographically heterogeneous genomic origins". Published in Genome Biology Use the following command to put the pieces together: % cat * &gt;./My_complete_data.txt The scripts used to analyze and plot the data are available in GitHub: https://github.com/AnaPoets/BarleyLandraces
DOI: 10.6084/m9.figshare.1466921.v2
title: Rawdata_03 - Barley landraces are characterized by geographically heterogeneous genomic origins

description: Genotyping data for landrace and cultivated lines from the National Small Grains Collection. The dataset has been devided in 11 parts. <strong>This is part 03. Make sure to download all 11 parts.</strong> Data used in the article: "Barley landraces are characterized by geographically heterogeneous genomic origins". Published in Genome Biology Use the following command to put the pieces together: % cat * &gt;./My_complete_data.txt The scripts used to analyze and plot the data are available in GitHub: https://github.com/AnaPoets/BarleyLandraces
DOI: 10.6084/m9.figshare.1466922.v2
title: Rawdata_04 - Barley landraces are characterized by geographically heterogeneous genomic origins

description: Genotyping data for landrace and cultivated lines from the National Small Grains Collection. The dataset has been devided in 11 parts. <strong>This is part 04. Make sure to download all 11 parts.</strong> Data used in the article: "Barley landraces are characterized by geographically heterogeneous genomic origins". Published in Genome Biology Use the following command to put the pieces together: % cat * &gt;./My_complete_data.txt The scripts used to analyze and plot the data are available in GitHub: https://github.com/AnaPoets/BarleyLandraces
DOI: 10.6084/m9.figshare.1466921.v1
title: Rawdata_03

description: Genotyping data for landrace and cultivated lines from the National Small Grains Collection. The dataset has been devided in 11 parts. <strong>This is part 03. Make sure to download all 11 parts.</strong> Data used in the article: "Barley landraces are characterized by geographically heterogeneous genomic origins". Published in Genome Biology Use the following command to put the pieces together: % cat * &gt;./My_complete_data.txt The scripts used to analyze and plot the data are available in GitHub: https://github.com/AnaPoets/BarleyLandraces
DOI: 10.6084/m9.figshare.1466922.v1
title: Rawdata_04

description: Genotyping data for landrace and cultivated lines from the National Small Grains Collection. The dataset has been devided in 11 parts. <strong>This is part 04. Make sure to download all 11 parts.</strong> Data used in the article: "Barley landraces are characterized by geographically heterogeneous genomic origins". Published in Genome Biology Use the following command to put the pieces together: % cat * &gt;./My_complete_data.txt The scripts used to analyze and plot the data are available in GitHub: https://github.com/AnaPoets/BarleyLandraces
DOI: 10.6084/m9.figshare.1466923.v2
title: Rawdata_05 - Barley landraces are characterized by geographically heterogeneous genomic origins

description: Genotyping data for landrace and cultivated lines from the National Small Grains Collection. The dataset has been devided in 11 parts. <strong>This is part 05. Make sure to download all 11 parts.</strong> Data used in the article: "Barley landraces are characterized by geographically heterogeneous genomic origins". Published in Genome Biology Use the following command to put the pieces together: % cat * &gt;./My_complete_data.txt The scripts used to analyze and plot the data are available in GitHub: https://github.com/AnaPoets/BarleyLandraces
DOI: 10.6084/m9.figshare.1466918
title: French contact matrices

description: French contact matrices for "all contact" and "physical contact only"
DOI: 10.6084/m9.figshare.1466919.v2
title: Rawdata_01 - Barley landraces are characterized by geographically heterogeneous genomic origins

description: Genotyping data for landrace and cultivated lines from the National Small Grains Collection. The dataset has been devided in 11 parts. <strong>This is part 01. Make sure to download all 11 parts.</strong> Data used in the article: "Barley landraces are characterized by geographically heterogeneous genomic origins". Published in Genome Biology Use the following command to put the pieces together: % cat * &gt;./My_complete_data.txt The scripts used to analyze and plot the data are available in GitHub: https://github.com/AnaPoets/BarleyLandraces
DOI: 10.6084/m9.figshare.1466923.v1
title: Rawdata_05

description: Genotyping data for landrace and cultivated lines from the National Small Grains Collection. The dataset has been devided in 11 parts. <strong>This is part 05. Make sure to download all 11 parts.</strong> Data used in the article: "Barley landraces are characterized by geographically heterogeneous genomic origins". Published in Genome Biology Use the following command to put the pieces together: % cat * &gt;./My_complete_data.txt The scripts used to analyze and plot the data are available in GitHub: https://github.com/AnaPoets/BarleyLandraces
DOI: 10.6084/m9.figshare.1466919.v1
title: Rawdata_01

description: Genotyping data for landrace and cultivated lines from the National Small Grains Collection. The dataset has been devided in 11 parts. <strong>This is part 01. Make sure to download all 11 parts.</strong> Data used in the article: "Barley landraces are characterized by geographically heterogeneous genomic origins". Published in Genome Biology Use the following command to put the pieces together: % cat * &gt;./My_complete_data.txt The scripts used to analyze and plot the data are available in GitHub: https://github.com/AnaPoets/BarleyLandraces
DOI: 10.6084/m9.figshare.1466915
title: Data file in SAS format

description: data file in SAS format
DOI: 10.6084/m9.figshare.1466916
title: Count of missing data for the SAS datafile

description: Missing data counting for the SAS datafile
DOI: 10.6084/m9.figshare.1466920.v2
title: Rawdata_02 - Barley landraces are characterized by geographically heterogeneous genomic origins

description: Genotyping data for landrace and cultivated lines from the National Small Grains Collection. The dataset has been devided in 11 parts. <strong>This is part 02. Make sure to download all 11 parts.</strong> Data used in the article: "Barley landraces are characterized by geographically heterogeneous genomic origins". Published in Genome Biology Use the following command to put the pieces together: % cat * &gt;./My_complete_data.txt The scripts used to analyze and plot the data are available in GitHub: https://github.com/AnaPoets/BarleyLandraces
DOI: 10.6084/m9.figshare.1466914
title: An RNA-Sequencing Study of the Genes and Metabolic Pathways Involved in <i>Aspergillus niger</i> Weathering of Potassium Feldspar

description: Microbial transformation of potassium feldspar to produce organic composite potassium fertilizer is recognized to be an important method of effective use of the huge reserves of low grade K<sup>+</sup>-bearing rock in China. The mechanism underlying microbial weathering of silicate minerals is still unclear, and this is an obstacle to practical methods of application. To thoroughly understand the molecular mechanism responsible for the weathering of potassium feldspar by <i>Aspergillus niger</i> at a molecular level, high-throughput RNA-sequencing (RNA-seq) and treatment with different potassium sources (cultured in Czapek medium with soluble K<sup>+</sup> or potassium feldspar) were used to investigate the differentially expressed genes of <i>A</i>. <i>niger</i> associated with potassium feldspar weathering and the related metabolic pathways. A series of differentially expressed genes related to the synthesis and transportation of organic acids, polysaccharides, and proteins (enzymes) were found to be closely associated with the K<sup>+</sup> released from minerals through bioinformatic analysis. In addition, 12 genes that showed apparent expression differences by RNA-seq analysis and are relevant to organic acid synthesis, protein modification, maintenance of cellular homeostasis, and material transportation, were selected to be further verified using RT-qPCR. Compared to the fungal samples cultured with soluble K<sup>+</sup>, those with potassium feldspar have certain genes that are more up-regulated, such as the genes for Na<sup>+</sup>,K<sup>+</sup>-ATPase (447.6 multiples), cystathionine beta-synthase (5.6 multiples), cysteine synthase (9 multiples), and glutathione synthase (3.5 multiples). The analysis indicates that <i>A. niger</i> weathering of potassium feldspar is due to the synergistic effect of many factors including the up-regulation of certain genes and activation of related metabolite pathways. The research improves our understanding of the mechanisms of microbial weathering of silicate minerals.
DOI: 10.6084/m9.figshare.1466916.v1
title: Count of missing data for the SAS datafile

description: Missing data counting for the SAS datafile
DOI: 10.6084/m9.figshare.1466920.v1
title: Rawdata_02

description: Genotyping data for landrace and cultivated lines from the National Small Grains Collection. The dataset has been devided in 11 parts. <strong>This is part 02. Make sure to download all 11 parts.</strong> Data used in the article: "Barley landraces are characterized by geographically heterogeneous genomic origins". Published in Genome Biology Use the following command to put the pieces together: % cat * &gt;./My_complete_data.txt The scripts used to analyze and plot the data are available in GitHub: https://github.com/AnaPoets/BarleyLandraces
DOI: 10.6084/m9.figshare.1466917.v1
title: Data file for Comes-F

description: This data set represent the raw data used to develop the first french contact matrices
DOI: 10.6084/m9.figshare.1466911
title: Passenger strand loading in overexpression experiments using microRNA mimics

description: MicroRNAs (miRNAs) are important regulators of gene function and manipulation of miRNAs is a central component of basic research. Modulation of gene expression by miRNA gain-of-function can be based on different approaches including transfection with miRNA mimics; artificial, chemically modified miRNA-like small RNAs. These molecules are intended to mimic the function of a miRNA guide strand while bypassing the maturation steps of endogenous miRNAs. Due to easy accessibility through commercial providers this approach has gained popularity, and accuracy is often assumed without prior independent testing. Our <i>in silico</i> analysis of over-represented sequence motifs in microarray expression data and sequencing of AGO-associated small RNAs indicate, however, that miRNA mimics may be associated with considerable side-effects due to the unwanted activity of the miRNA mimic complementary strand.
DOI: 10.6084/m9.figshare.1466914.v1
title: An RNA-Sequencing Study of the Genes and Metabolic Pathways Involved in <i>Aspergillus niger</i> Weathering of Potassium Feldspar

description: Microbial transformation of potassium feldspar to produce organic composite potassium fertilizer is recognized to be an important method of effective use of the huge reserves of low grade K<sup>+</sup>-bearing rock in China. The mechanism underlying microbial weathering of silicate minerals is still unclear, and this is an obstacle to practical methods of application. To thoroughly understand the molecular mechanism responsible for the weathering of potassium feldspar by <i>Aspergillus niger</i> at a molecular level, high-throughput RNA-sequencing (RNA-seq) and treatment with different potassium sources (cultured in Czapek medium with soluble K<sup>+</sup> or potassium feldspar) were used to investigate the differentially expressed genes of <i>A</i>. <i>niger</i> associated with potassium feldspar weathering and the related metabolic pathways. A series of differentially expressed genes related to the synthesis and transportation of organic acids, polysaccharides, and proteins (enzymes) were found to be closely associated with the K<sup>+</sup> released from minerals through bioinformatic analysis. In addition, 12 genes that showed apparent expression differences by RNA-seq analysis and are relevant to organic acid synthesis, protein modification, maintenance of cellular homeostasis, and material transportation, were selected to be further verified using RT-qPCR. Compared to the fungal samples cultured with soluble K<sup>+</sup>, those with potassium feldspar have certain genes that are more up-regulated, such as the genes for Na<sup>+</sup>,K<sup>+</sup>-ATPase (447.6 multiples), cystathionine beta-synthase (5.6 multiples), cysteine synthase (9 multiples), and glutathione synthase (3.5 multiples). The analysis indicates that <i>A. niger</i> weathering of potassium feldspar is due to the synergistic effect of many factors including the up-regulation of certain genes and activation of related metabolite pathways. The research improves our understanding of the mechanisms of microbial weathering of silicate minerals.
DOI: 10.6084/m9.figshare.1466911.v1
title: Passenger strand loading in overexpression experiments using microRNA mimics

description: MicroRNAs (miRNAs) are important regulators of gene function and manipulation of miRNAs is a central component of basic research. Modulation of gene expression by miRNA gain-of-function can be based on different approaches including transfection with miRNA mimics; artificial, chemically modified miRNA-like small RNAs. These molecules are intended to mimic the function of a miRNA guide strand while bypassing the maturation steps of endogenous miRNAs. Due to easy accessibility through commercial providers this approach has gained popularity, and accuracy is often assumed without prior independent testing. Our <i>in silico</i> analysis of over-represented sequence motifs in microarray expression data and sequencing of AGO-associated small RNAs indicate, however, that miRNA mimics may be associated with considerable side-effects due to the unwanted activity of the miRNA mimic complementary strand.
DOI: 10.6084/m9.figshare.1466914.v3
title: An RNA-Sequencing Study of the Genes and Metabolic Pathways Involved in <i>Aspergillus niger</i> Weathering of Potassium Feldspar

description: Microbial transformation of potassium feldspar to produce organic composite potassium fertilizer is recognized to be an important method of effective use of the huge reserves of low grade K<sup>+</sup>-bearing rock in China. The mechanism underlying microbial weathering of silicate minerals is still unclear, and this is an obstacle to practical methods of application. To thoroughly understand the molecular mechanism responsible for the weathering of potassium feldspar by <i>Aspergillus niger</i> at a molecular level, high-throughput RNA-sequencing (RNA-seq) and treatment with different potassium sources (cultured in Czapek medium with soluble K<sup>+</sup> or potassium feldspar) were used to investigate the differentially expressed genes of <i>A</i>. <i>niger</i> associated with potassium feldspar weathering and the related metabolic pathways. A series of differentially expressed genes related to the synthesis and transportation of organic acids, polysaccharides, and proteins (enzymes) were found to be closely associated with the K<sup>+</sup> released from minerals through bioinformatic analysis. In addition, 12 genes that showed apparent expression differences by RNA-seq analysis and are relevant to organic acid synthesis, protein modification, maintenance of cellular homeostasis, and material transportation, were selected to be further verified using RT-qPCR. Compared to the fungal samples cultured with soluble K<sup>+</sup>, those with potassium feldspar have certain genes that are more up-regulated, such as the genes for Na<sup>+</sup>,K<sup>+</sup>-ATPase (447.6 multiples), cystathionine beta-synthase (5.6 multiples), cysteine synthase (9 multiples), and glutathione synthase (3.5 multiples). The analysis indicates that <i>A. niger</i> weathering of potassium feldspar is due to the synergistic effect of many factors including the up-regulation of certain genes and activation of related metabolite pathways. The research improves our understanding of the mechanisms of microbial weathering of silicate minerals.
DOI: 10.6084/m9.figshare.1466911.v2
title: Passenger strand loading in overexpression experiments using microRNA mimics

description: MicroRNAs (miRNAs) are important regulators of gene function and manipulation of miRNAs is a central component of basic research. Modulation of gene expression by miRNA gain-of-function can be based on different approaches including transfection with miRNA mimics; artificial, chemically modified miRNA-like small RNAs. These molecules are intended to mimic the function of a miRNA guide strand while bypassing the maturation steps of endogenous miRNAs. Due to easy accessibility through commercial providers this approach has gained popularity, and accuracy is often assumed without prior independent testing. Our <i>in silico</i> analysis of over-represented sequence motifs in microarray expression data and sequencing of AGO-associated small RNAs indicate, however, that miRNA mimics may be associated with considerable side-effects due to the unwanted activity of the miRNA mimic complementary strand.
DOI: 10.6084/m9.figshare.1466914.v2
title: An RNA-Sequencing Study of the Genes and Metabolic Pathways Involved in <i>Aspergillus niger</i> Weathering of Potassium Feldspar

description: Microbial transformation of potassium feldspar to produce organic composite potassium fertilizer is recognized to be an important method of effective use of the huge reserves of low grade K<sup>+</sup>-bearing rock in China. The mechanism underlying microbial weathering of silicate minerals is still unclear, and this is an obstacle to practical methods of application. To thoroughly understand the molecular mechanism responsible for the weathering of potassium feldspar by <i>Aspergillus niger</i> at a molecular level, high-throughput RNA-sequencing (RNA-seq) and treatment with different potassium sources (cultured in Czapek medium with soluble K<sup>+</sup> or potassium feldspar) were used to investigate the differentially expressed genes of <i>A</i>. <i>niger</i> associated with potassium feldspar weathering and the related metabolic pathways. A series of differentially expressed genes related to the synthesis and transportation of organic acids, polysaccharides, and proteins (enzymes) were found to be closely associated with the K<sup>+</sup> released from minerals through bioinformatic analysis. In addition, 12 genes that showed apparent expression differences by RNA-seq analysis and are relevant to organic acid synthesis, protein modification, maintenance of cellular homeostasis, and material transportation, were selected to be further verified using RT-qPCR. Compared to the fungal samples cultured with soluble K<sup>+</sup>, those with potassium feldspar have certain genes that are more up-regulated, such as the genes for Na<sup>+</sup>,K<sup>+</sup>-ATPase (447.6 multiples), cystathionine beta-synthase (5.6 multiples), cysteine synthase (9 multiples), and glutathione synthase (3.5 multiples). The analysis indicates that <i>A. niger</i> weathering of potassium feldspar is due to the synergistic effect of many factors including the up-regulation of certain genes and activation of related metabolite pathways. The research improves our understanding of the mechanisms of microbial weathering of silicate minerals.
DOI: 10.6084/m9.figshare.1466904
title: Figure 3

description: Data for Figure 3
DOI: 10.6084/m9.figshare.1466904.v1
title: Figure 3

description: Data for Figure 3
DOI: 10.6084/m9.figshare.1466911.v3
title: Passenger strand loading in overexpression experiments using microRNA mimics

description: MicroRNAs (miRNAs) are important regulators of gene function and manipulation of miRNAs is a central component of basic research. Modulation of gene expression by miRNA gain-of-function can be based on different approaches including transfection with miRNA mimics; artificial, chemically modified miRNA-like small RNAs. These molecules are intended to mimic the function of a miRNA guide strand while bypassing the maturation steps of endogenous miRNAs. Due to easy accessibility through commercial providers this approach has gained popularity, and accuracy is often assumed without prior independent testing. Our <i>in silico</i> analysis of over-represented sequence motifs in microarray expression data and sequencing of AGO-associated small RNAs indicate, however, that miRNA mimics may be associated with considerable side-effects due to the unwanted activity of the miRNA mimic complementary strand.
DOI: 10.6084/m9.figshare.1466911.v4
title: Passenger strand loading in overexpression experiments using microRNA mimics

description: MicroRNAs (miRNAs) are important regulators of gene function and manipulation of miRNAs is a central component of basic research. Modulation of gene expression by miRNA gain-of-function can be based on different approaches including transfection with miRNA mimics; artificial, chemically modified miRNA-like small RNAs. These molecules are intended to mimic the function of a miRNA guide strand while bypassing the maturation steps of endogenous miRNAs. Due to easy accessibility through commercial providers this approach has gained popularity, and accuracy is often assumed without prior independent testing. Our <i>in silico</i> analysis of over-represented sequence motifs in microarray expression data and sequencing of AGO-associated small RNAs indicate, however, that miRNA mimics may be associated with considerable side-effects due to the unwanted activity of the miRNA mimic complementary strand.