cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8065816
title: Selective control of transposable element expression during T cell exhaustion and anti-PD1 treatment

description: Supplementary data from (Bonté et al.) which contains Human and Mouse RNA-seq data including : <strong>Raw counts and TPM/FPKM expression matrices of data analyzed </strong>(genes, individual TEs, TE subfamilies) raw.counts / fpkm.count / tpm.counts rds files <strong>SQuiRE raw output files </strong> SQuiRE.results rds files <strong>Seurat processed single cell object</strong> (with genes, TEs, Subfamilies) SC.object rds files In details, Mouse and Human data are labelled as follows : <strong>Mouse.SC :</strong> <strong>Type of data</strong> : Single cell RNA-seq data of sorted CD8+ TILs (model B16 melanoma tumors ) <strong>Label of samples </strong>: Naïve like, Early activated, EffectorMemory, Tpex, Tex <strong>Origin of the data</strong> : S. J. Carmona, I. Siddiqui, M. Bilous, W. Held, D. Gfeller, Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq. Oncoimmunology 9, 1737369 (2020). <strong>Mouse.tumor.TILs :</strong> <strong>Type of data</strong> : bulk RNA-seq data of sorted CD8+ TILs (model B16 melanoma tumors) <strong>Label of samples </strong>: Tumor Slamf6+ or Tumor Tim3+ <strong>Origin of the data</strong> : B. C. Miller<em> et al.</em>, Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade. <em>Nature Immunology</em> <strong>20</strong>, 326-336 (2019). <strong>Mouse.LCMV.TILs :</strong> <strong>Type of data</strong> : bulk RNA-seq data of sorted CD8+ TILs (model LCMV clone 13) <strong>Label of samples </strong>: LCMV Slamf6+ or LCMV Tim3+ <strong>Origin of the data</strong> : B. C. Miller<em> et al.</em>, Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade. <em>Nature Immunology</em> <strong>20</strong>, 326-336 (2019). <strong>Mouse.LCMV_Fli1.TILs :</strong> <strong>Type of data</strong> : bulk RNA-seq data of sorted CD8+ TILs (model LCMV clone 13) <strong>Label of samples </strong>: WT or Fli1KO <strong>Origin of the data</strong> : Z. Chen<em> et al.</em>, In vivo CD8(+) T cell CRISPR screening reveals control by Fli1 in infection and cancer. <em>Cell</em> <strong>184</strong>, 1262-1280 e1222 (2021). <strong>Human.TILs </strong>: <strong>Type of data</strong> : bulk RNA-seq data of sorted CD8+ TILs (NSCLC tumor tissue ) <strong>Label of samples </strong>: Tex or Tpex <strong>Origin of the data</strong> : Bonté et al. (ongoing submission) Type of features is labeled as follows: <strong>Gene expression</strong> : genes <strong>Individual TE expression</strong> : TEs <strong>TE subfamiliy expression</strong> : SF Metadata corresponding to each expression matrix can be found here.
DOI: 10.5281/zenodo.8065815
title: Selective control of transposable element expression during T cell exhaustion and anti-PD1 treatment

description: Supplementary data from (Bonté et al.) which contains Human and Mouse RNA-seq data including : <strong>Raw counts and TPM/FPKM expression matrices of data analyzed </strong>(genes, individual TEs, TE subfamilies) raw.counts / fpkm.count / tpm.counts rds files <strong>SQuiRE raw output files </strong> SQuiRE.results rds files <strong>Seurat processed single cell object</strong> (with genes, TEs, Subfamilies) SC.object rds files In details, Mouse and Human data are labelled as follows : <strong>Mouse.SC :</strong> <strong>Type of data</strong> : Single cell RNA-seq data of sorted CD8+ TILs (model B16 melanoma tumors ) <strong>Label of samples </strong>: Naïve like, Early activated, EffectorMemory, Tpex, Tex <strong>Origin of the data</strong> : S. J. Carmona, I. Siddiqui, M. Bilous, W. Held, D. Gfeller, Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq. Oncoimmunology 9, 1737369 (2020). <strong>Mouse.tumor.TILs :</strong> <strong>Type of data</strong> : bulk RNA-seq data of sorted CD8+ TILs (model B16 melanoma tumors) <strong>Label of samples </strong>: Tumor Slamf6+ or Tumor Tim3+ <strong>Origin of the data</strong> : B. C. Miller<em> et al.</em>, Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade. <em>Nature Immunology</em> <strong>20</strong>, 326-336 (2019). <strong>Mouse.LCMV.TILs :</strong> <strong>Type of data</strong> : bulk RNA-seq data of sorted CD8+ TILs (model LCMV clone 13) <strong>Label of samples </strong>: LCMV Slamf6+ or LCMV Tim3+ <strong>Origin of the data</strong> : B. C. Miller<em> et al.</em>, Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade. <em>Nature Immunology</em> <strong>20</strong>, 326-336 (2019). <strong>Mouse.LCMV_Fli1.TILs :</strong> <strong>Type of data</strong> : bulk RNA-seq data of sorted CD8+ TILs (model LCMV clone 13) <strong>Label of samples </strong>: WT or Fli1KO <strong>Origin of the data</strong> : Z. Chen<em> et al.</em>, In vivo CD8(+) T cell CRISPR screening reveals control by Fli1 in infection and cancer. <em>Cell</em> <strong>184</strong>, 1262-1280 e1222 (2021). <strong>Human.TILs </strong>: <strong>Type of data</strong> : bulk RNA-seq data of sorted CD8+ TILs (NSCLC tumor tissue ) <strong>Label of samples </strong>: Tex or Tpex <strong>Origin of the data</strong> : Bonté et al. (ongoing submission) Type of features is labeled as follows: <strong>Gene expression</strong> : genes <strong>Individual TE expression</strong> : TEs <strong>TE subfamiliy expression</strong> : SF Metadata corresponding to each expression matrix can be found here.
DOI: 10.34740/kaggle/dsv/6053666
title: Mahanagar Yatayat Dataset
DOI: 10.5517/ccdc.csd.cc1yz9jr
title: CCDC 1816585: Experimental Crystal Structure Determination

description: Related Article: Yu Xiong, Zheng Zhao, Weijun Zhao, Huili Ma, Qian Peng, Zikai He, Xuepeng Zhang, Yuncong Chen, Xuewen He, Jacky W. Y. Lam, Ben Zhong Tang|2018|Angew.Chem.,Int.Ed.|57|7997|doi:10.1002/anie.201800834
description: Related Article: Yu Xiong, Junyi Gong, Junkai Liu, Deliang Wang, Hongzhuo Wu, Zheng Zhao, Manman Fang, Zhen Li, Dong Wang, Ben Zhong Tang|2022|J.Mater.Chem.C|10|10009|doi:10.1039/D2TC01857H
description: Related Article: Yu Xiong, Junyi Gong, Junkai Liu, Deliang Wang, Hongzhuo Wu, Zheng Zhao, Manman Fang, Zhen Li, Dong Wang, Ben Zhong Tang|2022|J.Mater.Chem.C|10|10009|doi:10.1039/D2TC01857H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1yz9lt
title: CCDC 1816587: Experimental Crystal Structure Determination

description: Related Article: Yu Xiong, Zheng Zhao, Weijun Zhao, Huili Ma, Qian Peng, Zikai He, Xuepeng Zhang, Yuncong Chen, Xuewen He, Jacky W. Y. Lam, Ben Zhong Tang|2018|Angew.Chem.,Int.Ed.|57|7997|doi:10.1002/anie.201800834
description: Related Article: Yu Xiong, Junyi Gong, Junkai Liu, Deliang Wang, Hongzhuo Wu, Zheng Zhao, Manman Fang, Zhen Li, Dong Wang, Ben Zhong Tang|2022|J.Mater.Chem.C|10|10009|doi:10.1039/D2TC01857H
description: Related Article: Yu Xiong, Junyi Gong, Junkai Liu, Deliang Wang, Hongzhuo Wu, Zheng Zhao, Manman Fang, Zhen Li, Dong Wang, Ben Zhong Tang|2022|J.Mater.Chem.C|10|10009|doi:10.1039/D2TC01857H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1yz9ks
title: CCDC 1816586: Experimental Crystal Structure Determination

description: Related Article: Yu Xiong, Zheng Zhao, Weijun Zhao, Huili Ma, Qian Peng, Zikai He, Xuepeng Zhang, Yuncong Chen, Xuewen He, Jacky W. Y. Lam, Ben Zhong Tang|2018|Angew.Chem.,Int.Ed.|57|7997|doi:10.1002/anie.201800834
description: Related Article: Yu Xiong, Junyi Gong, Junkai Liu, Deliang Wang, Hongzhuo Wu, Zheng Zhao, Manman Fang, Zhen Li, Dong Wang, Ben Zhong Tang|2022|J.Mater.Chem.C|10|10009|doi:10.1039/D2TC01857H
description: Related Article: Yu Xiong, Junyi Gong, Junkai Liu, Deliang Wang, Hongzhuo Wu, Zheng Zhao, Manman Fang, Zhen Li, Dong Wang, Ben Zhong Tang|2022|J.Mater.Chem.C|10|10009|doi:10.1039/D2TC01857H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.23600949
title: ACCELEROMETER CALIBRATION RESULTS AT KENYA BUREAU OF STANDARDS.docx

description: This data is about the comparative results of calibration of the dgitial sensors at the Kenya Bureau of Standards,KENYA.
DOI: 10.5281/zenodo.4475680
title: QTL summary statistics from the DIRECT consortium

description: These are the complete summary statistics for DIRECT genotype-phenotypes associations (QTLs). The project performed genotype-phenotype associations for gene expression (RNAseq), targeted proteins (Olink), targeted metabolites (Biocrates) and untargeted metabolites (Metabolon) derived from 3,029 blood and plasma samples from the DIRECT cohort. This submission includes supplementary files and nominal pvalues (as uncorrected pvalues) for all associations included in the manuscript. Trans associations included are typically limited to pvalues &lt;1e-04. Network tables are also included, with information to load and use Cytoscape to visualize them. This is version 2, some files were missing on version 1.
DOI: 10.5281/zenodo.4475681
title: QTL summary statistics from the DIRECT consortium

description: These are the complete summary statistics for DIRECT genotype-phenotypes associations (QTLs). The project performed genotype-phenotype associations for gene expression (RNAseq), targeted proteins (Olink), targeted metabolites (Biocrates) and untargeted metabolites (Metabolon) derived from 3,029 blood and plasma samples from the DIRECT cohort. This submission includes supplementary files and nominal pvalues (as uncorrected pvalues) for all associations included in the manuscript. Trans associations included are typically limited to pvalues &lt;1e-04. Network tables are also included, with information to load and use Cytoscape to visualize them.
DOI: 10.5281/zenodo.7521410
title: QTL summary statistics from the DIRECT consortium

description: These are the complete summary statistics for DIRECT genotype-phenotypes associations (QTLs). The project performed genotype-phenotype associations for gene expression (RNAseq), targeted proteins (Olink), targeted metabolites (Biocrates) and untargeted metabolites (Metabolon) derived from 3,029 blood and plasma samples from the DIRECT cohort. This submission includes supplementary files and nominal pvalues (as uncorrected pvalues) for all associations included in the manuscript. Trans associations included are typically limited to pvalues &lt;1e-04. Network tables are also included, with information to load and use Cytoscape to visualize them. This is version 2, some files were missing on version 1.
DOI: 10.25919/f6wp-a075
title: Parkes observations for project P1183 semester 2023APRS_11

description: A new energetic repeating FRB 20220529 can be observed by both FAST and Parkes telescopes and the simultaneous observing time is up to one hour. We have observed this source using Parkes UWL green time and in total 21 bursts have been detected. Two bursts of them have the corresponding simultaneous FAST observations. Only one burst has 4-pol datasets and is bright enough to analyse the polarization properties. Therefore, we propose to continue the monitoring of the source of FRB 20220529 using the Parkes UWL with high-time resolution and 4-pol observation. The new proposed observation aims to: (1)detect more bursts by Parkes UWL with full polarization information; (2) detect more bursts by Parkes UWL with corresponding simultaneous FAST observations; (3) study the radiation spectrum by more bursts detected in simultaneous observations of Parkes and FAST; (4) study the burst microstructure using high time resolution datasets, and (5) study the frequency ranges changes of the repeating bursts.
DOI: 10.5281/zenodo.8096305
title: RNA-Seq data from: Hox genes modulate physical forces to differentially shape small and large intestinal epithelia

description: Hox genes are highly conserved, master regulators of spatial patterning in the embryo, but how these factors trigger regional morphogenesis has largely remained a mystery. In the developing gut, Hox genes help demarcate identities of the small and large intestines early in embryogenesis, which ultimately leads to their specialization in both form and function. While the midgut forms villi, the hindgut develops flat, brain-like sulci that resolve into heterogeneous outgrowths. Combining mechanical measurements and mathematical modeling, we demonstrate that the posterior Hox gene Hoxd13 regulates biophysical phenomena that shape the hindgut lumen. We further show that Hoxd13 acts through the TGFβ pathway to thicken, stiffen, and promote isotropic growth of the subepithelial mesenchyme; together, these features lead to hindgut surface buckling. TGFβ, in turn, promotes collagen deposition to affect mesenchymal geometry and growth. We thus identify a cascade of events downstream of positional genetic identity that direct posterior intestinal morphogenesis. To identify genes and pathways that are directly or indirectly regulated by Hoxd13 to affect posterior gut morphogenesis in the chick, we compared mesodermal transcriptomes of wild-type midgut and hindgut intestinal samples, as well as mesodermal samples from a Hoxd13-overexpressing midgut at E12 and E14. Tissues were dissected and endoderm layers were removed manually before RNA extraction and downstream processing. Unbiased clustering was used to identify genes commonly differentially expressed in the hindgut and Hoxd13-misexpressing midgut. This submission contains bulk RNA-seq raw data (fastq.bz2 files) and processed .txt files with read counts. Experiment information is provided in .xlsx Metadata file used for NCBI GEO submission.
DOI: 10.5281/zenodo.8096304
title: RNA-Seq data from: Hox genes modulate physical forces to differentially shape small and large intestinal epithelia

description: Hox genes are highly conserved, master regulators of spatial patterning in the embryo, but how these factors trigger regional morphogenesis has largely remained a mystery. In the developing gut, Hox genes help demarcate identities of the small and large intestines early in embryogenesis, which ultimately leads to their specialization in both form and function. While the midgut forms villi, the hindgut develops flat, brain-like sulci that resolve into heterogeneous outgrowths. Combining mechanical measurements and mathematical modeling, we demonstrate that the posterior Hox gene Hoxd13 regulates biophysical phenomena that shape the hindgut lumen. We further show that Hoxd13 acts through the TGFβ pathway to thicken, stiffen, and promote isotropic growth of the subepithelial mesenchyme; together, these features lead to hindgut surface buckling. TGFβ, in turn, promotes collagen deposition to affect mesenchymal geometry and growth. We thus identify a cascade of events downstream of positional genetic identity that direct posterior intestinal morphogenesis. To identify genes and pathways that are directly or indirectly regulated by Hoxd13 to affect posterior gut morphogenesis in the chick, we compared mesodermal transcriptomes of wild-type midgut and hindgut intestinal samples, as well as mesodermal samples from a Hoxd13-overexpressing midgut at E12 and E14. Tissues were dissected and endoderm layers were removed manually before RNA extraction and downstream processing. Unbiased clustering was used to identify genes commonly differentially expressed in the hindgut and Hoxd13-misexpressing midgut. This submission contains bulk RNA-seq raw data (fastq.bz2 files) and processed .txt files with read counts. Experiment information is provided in .xlsx Metadata file used for NCBI GEO submission.
DOI: 10.6084/m9.figshare.23600967
title: GEOTECHNICAL SOIL INVESTIGATION RESULTS.docx

description: The data is mainly the graphical results of geotechnical physical and mechanical soil properties.
DOI: 10.5281/zenodo.8096832
title: cumathamnion_decipiens_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8096831
title: cumathamnion_decipiens_spades_01.fasta.gz

description: .
DOI: 10.6084/m9.figshare.22352656
title: High time-resolved studies of stick-slip show similar dilatancy to fast and slow earthquakes

description: The data are from a suite of friction experiments performed on simulated fault gouges comprised of glass spheres, sheared in a ring-shear arrangement. We simultaneously recorded detailed mechanical data, acoustic emission and precise thickness variation of dense granular assemblies at an ultra-high sampling rate of 10 MHz. Experiments were performed at four effective normal stress of 900 kPa, 1100 kPa, 1300 kPa, and 1500 kPa. The shear velocity was set to 1.5 °/min.
DOI: 10.6084/m9.figshare.22352656.v1
title: High time-resolved studies of stick-slip show similar dilatancy to fast and slow earthquakes

description: The data are from a suite of friction experiments performed on simulated fault gouges comprised of glass spheres, sheared in a ring-shear arrangement. We simultaneously recorded detailed mechanical data, acoustic emission and precise thickness variation of dense granular assemblies at an ultra-high sampling rate of 10 MHz. Experiments were performed at four effective normal stress of 900 kPa, 1100 kPa, 1300 kPa, and 1500 kPa. The shear velocity was set to 1.5 °/min.
DOI: 10.6084/m9.figshare.22352656.v2
title: High time-resolved studies of stick-slip show similar dilatancy to fast and slow earthquakes

description: The data are from a suite of friction experiments performed on simulated fault gouges comprised of glass spheres, sheared in a ring-shear arrangement. We simultaneously recorded detailed mechanical data, acoustic emission and precise thickness variation of dense granular assemblies at an ultra-high sampling rate of 10 MHz. Experiments were performed at four effective normal stress of 900 kPa, 1100 kPa, 1300 kPa, and 1500 kPa. The shear velocity was set to 1.5 °/min.
DOI: 10.6084/m9.figshare.23600985
title: SUMMARY OF ATTERBERG LIMIT RESULTS.docx

description: The data provides the Atterberg values of the tested soil properties.
DOI: 10.5281/zenodo.5351449
title: [DATASET 9] - PLANT-ROBOT INTERFACES FOR ENERGY HARVESTING

description: In the framework of GrowBot project, task 7.2 aims at developing bio-hybrid energy harvesting systems based on the triboelectric effect.<br> The energy conversion occurs at plant leaves level during mechanical stimulation (i.e., wind, rain, etc.).<br> Two main components have been developed in GrowBot:<br> - Flexible artificial “leaves” (flexible electrodes covered with tailored materials) to enhance mechanical impacts with the plant leaves and further enhance power output.<br> - Minimal-invasive electrodes that establish electrical contact between GrowBots and real plants. DS9 aims at collecting all the experimental data gathered during these activities.
DOI: 10.5281/zenodo.5353663
title: [DATASET 9] - PLANT-ROBOT INTERFACES FOR ENERGY HARVESTING

description: In the framework of GrowBot project, task 7.2 aims at developing bio-hybrid energy harvesting systems based on the triboelectric effect.<br> The energy conversion occurs at plant leaves level during mechanical stimulation (i.e., wind, rain, etc.).<br> Two main components have been developed in GrowBot:<br> - Flexible artificial “leaves” (flexible electrodes covered with tailored materials) to enhance mechanical impacts with the plant leaves and further enhance power output.<br> - Minimal-invasive electrodes that establish electrical contact between GrowBots and real plants. DS9 aims at collecting all the experimental data gathered during these activities.
DOI: 10.5281/zenodo.5351448
title: [DATASET 9] - PLANT-ROBOT INTERFACES FOR ENERGY HARVESTING

description: In the framework of GrowBot project, task 7.2 aims at developing bio-hybrid energy harvesting systems based on the triboelectric effect.<br> The energy conversion occurs at plant leaves level during mechanical stimulation (i.e., wind, rain, etc.).<br> Two main components have been developed in GrowBot:<br> - Flexible artificial “leaves” (flexible electrodes covered with tailored materials) to enhance mechanical impacts with the plant leaves and further enhance power output.<br> - Minimal-invasive electrodes that establish electrical contact between GrowBots and real plants. DS9 aims at collecting all the experimental data gathered during these activities.
DOI: 10.5281/zenodo.8096846
title: [DATASET 9] - PLANT-ROBOT INTERFACES FOR ENERGY HARVESTING

description: In the framework of GrowBot project, task 7.2 aims at developing bio-hybrid energy harvesting systems based on the triboelectric effect.<br> The energy conversion occurs at plant leaves level during mechanical stimulation (i.e., wind, rain, etc.).<br> Two main components have been developed in GrowBot:<br> - Flexible artificial “leaves” (flexible electrodes covered with tailored materials) to enhance mechanical impacts with the plant leaves and further enhance power output.<br> - Minimal-invasive electrodes that establish electrical contact between GrowBots and real plants. DS9 aims at collecting all the experimental data gathered during these activities.
DOI: 10.5517/ccdc.csd.cc2dldzd
title: CCDC 2222234: Experimental Crystal Structure Determination

description: Related Article: Yiwei Zhou, Christian D. Buch, Steen H. Hansen, Stergios Piligkos|2023|Dalton Trans.|52|8792|doi:10.1039/D3DT01191G
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.8096635
title: Dataset S3

description: Dataset S3 contains R code in the file DatasetS3.Rmd and all the necessary raw data files needed to complete the statistical analyses and generate the figures in the manuscript, “Evolutionary retention of chemically diverse terpene nucleosides in bacteria that cause tuberculosis”. To run the R code, the file paths in the R code must be revised to match the correct file path. The R Markdown can be knitted into the included HTML report Dataset.html, or output as individual PDF files.
DOI: 10.5281/zenodo.8096634
title: Dataset S3

description: Dataset S3 contains R code in the file DatasetS3.Rmd and all the necessary raw data files needed to complete the statistical analyses and generate the figures in the manuscript, “Evolutionary retention of chemically diverse terpene nucleosides in bacteria that cause tuberculosis”. To run the R code, the file paths in the R code must be revised to match the correct file path. The R Markdown can be knitted into the included HTML report Dataset.html, or output as individual PDF files.
DOI: 10.6084/m9.figshare.23600988
title: SUMMARY OF MECHANICAL PROPERTIES OF THE SOIL.docx

description: The data is about soil mechanical properties that include Young's Modulus,Poisson's ratio,California Bearing ratio,Shear Strength