cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.vxmnte
title: Occurrence Download

description: A dataset containing 56706 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Canada",
 "Geometry POLYGON((-66.4 43.4,-59.8 43.4,-59.8 47.1,-66.4 47.1,-66.4 43.4))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (EN, CR, EW, EX, VU)",
 "OccurrenceStatus is Present",
 "StateProvince is Nova Scotia",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 56706 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037991-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3643502_d1.v1
title: Additional file 3: of dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data

description: Methods 2. Instructions to reproduce main images. (MD 4 kb)
DOI: 10.6084/m9.figshare.c.3643502_d2.v1
title: Additional file 6: of dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data

description: Methods 3. Simulation of datasets and differential expression. (RMD 7 kb)
DOI: 10.6084/m9.figshare.c.3643502_d3.v1
title: Additional file 4: Table S1. of dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data

description: Mapping statistics of the data set used to generate Fig.Â 1. (CSV 520 bytes)
DOI: 10.6084/m9.figshare.c.3643502_d6.v1
title: Additional file 7: Table S2. of dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data

description: Full version of TableÂ 1 from manuscript. (CSV 2183 kb)
DOI: 10.6084/m9.figshare.c.3643565_d1.v1
title: MOESM2 of Optimized methods for extracting circulating small RNAs from long-term stored equine samples

description: Additional file 2. Serum RNA extraction results from 120 samples. A table in XLSX format with serum absorbances at 414Â nm, serum volume used, sample collection year, and RNA concentrations obtained using the optimized procedures and measured with Qubit and Bioanalyzer.
DOI: 10.6084/m9.figshare.c.3643565_d2.v1
title: MOESM3 of Optimized methods for extracting circulating small RNAs from long-term stored equine samples

description: Additional file 3. RNA extraction from EDTA. A table in XLSX format with RNA concentration and yield measured with Qubit, miRNA concentration measured with Bioanalyzer, and RNA quality number (RQN) measured by Fragment Analyzer in samples used for pilot experiments during method optimization and with already optimized method.
DOI: 10.6084/m9.figshare.c.3643565_d3.v1
title: MOESM1 of Optimized methods for extracting circulating small RNAs from long-term stored equine samples

description: Additional file 1. RNA extraction from serum. A table in XLSX format with RNA concentration and yield measured with Qubit, miRNA concentration and rRNA contamination measured with Bioanalyzer in samples used for pilot experiments during method optimization. Read numbers of the six samples sequenced are also given.
DOI: 10.6084/m9.figshare.c.3643574_d4.v1
title: Additional file 5: Figure S3. of Gene expression and functional annotation of human choroid plexus epithelium failure in Alzheimerâ  s disease

description: Downregulated genes in AD Br5â  6. The input genes Additional file 8: Table S4) are bioinformatically translated to proteins and the symbols are colored. Another set of genes/proteins is inserted by the knowledgedatabase to construct the most likely networks; the symbols are white. Different types of symbols exist (for explanation see www.ingenuity.com : transporters, strucural proteins, secreted proteins, etc). The symbols are connected by solid lines and dotted lines. These denote, respectively, direct physical/functional and indirect interaction between the symbols/genes/proteins. These interactions are, via the knowledgde database, derived form wet lab experiments in the literature, and from big data stored in curated public databases (GEO, etc). The most likely networks are constructed by the knowledge database, taken all available data into account of human, mouse, rat and in vitro model experiments. Finally, once the networks are constructed, specific entries in the networks can be labelled, by hand of the user, to specifically label molecules wihch are involved in sopecific diseases or biological process of interest. In this way, the (predicted) molecular enviroment of entries of interest can be explored. (ZIP 10804 kb)
DOI: 10.6084/m9.figshare.c.3643574_d3.v1
title: Additional file 10: Table S5. of Gene expression and functional annotation of human choroid plexus epithelium failure in Alzheimerâ  s disease

description: Presents the gene expressionÂ in our datasets of a number of previously known AD disease genes. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3643574_d5.v1
title: Additional file 6: Table S3. of Gene expression and functional annotation of human choroid plexus epithelium failure in Alzheimerâ  s disease

description: Contains the specifications of genes upregulated in CPE Br(5â  6) compared to CPE Br(0,1). (XLSX 26 kb)
DOI: 10.6084/m9.figshare.c.3643574_d8.v1
title: Additional file 8: Table S4. of Gene expression and functional annotation of human choroid plexus epithelium failure in Alzheimerâ  s disease

description: Contains the specifications of genes downregulated in CPE Br(5â  6) compared to CPE Br(0,1). (XLSX 31 kb)
DOI: 10.6084/m9.figshare.c.3643574_d7.v1
title: Additional file 3: Table S2. of Gene expression and functional annotation of human choroid plexus epithelium failure in Alzheimerâ  s disease

description: Contains compilations of lists of (disease) genes previously implicated in relevant disease. The entries are used to label the molecular network in Additional file 4: Figure S2Â and Additional file 5: Figure S3. (XLS 190 kb)
DOI: 10.6084/m9.figshare.c.3643574_d10.v1
title: Additional file 1: Tabel S1. of Gene expression and functional annotation of human choroid plexus epithelium failure in Alzheimerâ  s disease

description: Contains characteristics of donor eyes used. (XLS 25 kb)
DOI: 10.6084/m9.figshare.c.3643577_d1.v1
title: Additional file 1: of 
                     Dirofilaria infections in dogs in different areas of Greece

description: Data collected from the questionnaires filled in for each examined dog. (XLSX 91Â kb)
DOI: 10.15468/dl.wuchct
title: Occurrence Download

description: A dataset containing 497641 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2024-10-22",
 "EventDate is less than or equal to 2024-11-21",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 }
 ]
}

 The dataset includes 497641 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037979-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3643583_d1.v1
title: Additional file 10: Table S5. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

description: Detailed information on CRISPR/Cas9 cleavage efficiency studies. Number of guides, cell types, delivery, and expression method of the guide RNA and comments. (XLS 36 kb)
DOI: 10.6084/m9.figshare.c.3643583_d6.v1
title: Additional file 2: of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

description: Collection of all off-targets and their frequencies from all off-target studies. The fields of the table are: name of the guide (guide), its sequence (guideSeq), the sequence of the off-target (otSeq), the specificity score of the guide determined with up to four mismatches (guideSpecScore4MM), the GC content of the guide (guideGcCont), the fraction of reads or lentiviral integration sites for this off-target (readFraction), the number of mismatches of the off-target to the guide (mismatches), the Hsu et al. off-target score (outscore), a string indicating with stars where the mismatches are located over the length of the guide sequence (otLogo), the minimal number of mismatches if a deletion is allowed in the guide sequence (bulgeRnaMmCount), the guide sequence with this deletion marked in parentheses (bulgeRnaGuideSeq), the minimal number of mismatches if a deletion is allowed in the off-target sequence (bulgeDnaMmCount), and the off-target sequence with the deletion marked (bulgeDnaOtSeq). Bulge information is shown only if the number of mismatches obtained by the deletion is at least three less than the number of mismatches without the deletion; otherwise the fields are set to “−1”. (TSV 98 kb)
DOI: 10.6084/m9.figshare.c.3643583_d5.v1
title: Additional file 5: Table S3. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

description: Reproducibility of the guide VEGFA GGGTGGGGGGAGTTTGCTCCTGG across three different assays. Shown are the numbers and locations of the mismatches, the off-target score, the modification frequencies found by the different studies, and whether the off-target was predicted by the CRISPR Design website ( http://crispr.mit.edu/ ). (XLS 45 kb)
DOI: 10.6084/m9.figshare.c.3643583_d7.v1
title: Additional file 14: of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

description: Scatterplots of predicted versus obtained cleavage efficiency for all studies shown in Figs. 4 and 5 and Additional file 13: Figure S5 for all scoring models, including 3′ GC content-related heuristics. One row per dataset, one column per prediction score. The previously published datasets shown are, in order: the training data from the Wang, Doench 2014 (human and mouse) and Chari (293 T and K562) studies, Wang 2015, Doench 2016 (AZD and PLX treatment), Hart 2016 averaged over all time points (Rpe1 and the two Hct116 replicates), the data from studies by Moreno-Mateos, Varshney, Gagnon, Liu, Ren, Housden, Farboud, and Gandhi. For details and references on these datasets, see “Methods” or Additional file 10: Table S5. The last six rows represent datasets from this study: “Concordet” is a cell culture dataset quantified with T7 endonuclease and on gels, the datasets “Schönig” and “Eschstruth” ranked guides 1–3 by efficiency, “Shkumatava” by number of mutated sequencing clones obtained from zebrafish embryos, “Teboul” the percentage of mutant mouse embryos. For details on these datasets, see the “Methods” section and also Additional file 15: Table S7 for the Teboul dataset. (TSV 8773 kb)
DOI: 10.6084/m9.figshare.c.3643643_d3.v1
title: Additional file 9: of 
                     De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis

description: Alignment of O -methyltransferase proteins. (FASTA 25 kb)
DOI: 10.6084/m9.figshare.c.3643643_d2.v1
title: Additional file 8: Alignment of HPP dioxygenase proteins. of 
                     De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis

description: (FASTA 2 kb)
DOI: 10.6084/m9.figshare.28034723
title: dataset_1

description: E-courses 3 ECTS data calculation
DOI: 10.13020/8tj0-xt19
title: Data supporting the manuscript Role of microbial mats in bed evolution and the formation of sedimentary structures

description: This dataset contains the data collected and presented in the manuscript "Role of microbial mats in bed evolution and the formation of sedimentary structures". It includes the bed topographies along the centerline of the channel for each tested case. Additionally, it contains the matlab codes used to process the data.
description: The file named "Data.zip" contains 7 folders, each one containing a .mat file with the longitudinal position, bed elevation and time interval for both abiotic and biotic cases. The file "MatLab_Codes.zip" contains the matlab codes used to process the data.
DOI: 10.6084/m9.figshare.c.3643700_d1.v1
title: Additional file 1: Table S1. of Comprehensive genomic characterization of five canine lymphoid tumor cell lines

description: Known cancer-associated genes located in regions of genomic imbalance in each of the five cell lines. Table S2. Summary of fold changes of cancer-associated genes for each cell line when normalized expression level was compared with mean normalized expression levels of non-neoplastic lymph nodes. Table S3. List of 50 transcripts from each cell line with the largest absolute fold changes when normalized expression level was compared with mean normalized expression levels of non-neoplastic lymph nodes. Table S4. Gene ontology (GO) biological processes enriched for genes upregulated or downregulatued by &gt;5 fold in each cell line when compared with non-neoplastic lymph nodes. The top ten terms associated with up and down regulated genes are listed. Table S5. KEGG pathways associatated with genes upregulated or downregulated by &gt;5 fold in each cell line when compared with non-neoplastic lymph node. Up to the top ten pathways associated with up or down regulated genes are listed. (XLSX 113Â kb)
DOI: 10.5517/ccdc.csd.cc2h0phq
title: CCDC 2294573: Experimental Crystal Structure Determination

description: Related Article: Miljan Z. Ćorović, Madeleine A. Ehweiner, Peter E. Hartmann, Felix Sbüll, Ferdinand Belaj, A. Daniel Boese, Jesse Lepluart, Martin L. Kirk, Nadia C. Mösch-Zanetti|2024|J.Am.Chem.Soc.|146|32392|doi:10.1021/jacs.4c07724
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.cc2h1cxv
title: CCDC 2295237: Experimental Crystal Structure Determination

description: Related Article: Haitao Zhu, Houcong Li, Yuxin Ji, Min Hou, Qingling Yang, Lili Liang, Wenge Li|2024|Bioorg.Chem.|153|107949|doi:10.1016/j.bioorg.2024.107949
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.cc2h5sm3
title: CCDC 2299475: Experimental Crystal Structure Determination

description: Related Article: Anatolii S. Burlov, Valery G. Vlasenko, Yurii V. Koshchienko, Bogdan V. Chaltsev, Oleg P. Demidov, Alexandra A. Kolodina, Dmitrii A. Garnovskii, Elena V. Braga, Alexey N. Gusev, Wolfgang Linert|2024|Opt.Mater.|157|116412|doi:10.1016/j.optmat.2024.116412
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.cc2h5ss8
title: CCDC 2299480: Experimental Crystal Structure Determination

description: Related Article: Anatolii S. Burlov, Valery G. Vlasenko, Yurii V. Koshchienko, Bogdan V. Chaltsev, Oleg P. Demidov, Alexandra A. Kolodina, Dmitrii A. Garnovskii, Elena V. Braga, Alexey N. Gusev, Wolfgang Linert|2024|Opt.Mater.|157|116412|doi:10.1016/j.optmat.2024.116412
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.cc2j9t7x
title: CCDC 2333129: Experimental Crystal Structure Determination

description: Related Article: Gengxin Wu, Yong-Kang Zhu, Dongxia Li, Jia-Rui Wu, Yan Wang, Zhiquan Zhang, Ying-Wei Yang|2024|Inorg.Chem.Front.|11|8916|doi:10.1039/D4QI02422B
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.cc2jnydk
title: CCDC 2343829: Experimental Crystal Structure Determination

description: Related Article: Jieli Lin, Shihua Liu, Shunlin Zheng, Hansjörg Grützmacher, Cheng-Yong Su, Zhongshu Li|2024|Chemical Science|15|20030|doi:10.1039/D4SC06462C
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.cc2jnyfl
title: CCDC 2343830: Experimental Crystal Structure Determination

description: Related Article: Jieli Lin, Shihua Liu, Shunlin Zheng, Hansjörg Grützmacher, Cheng-Yong Su, Zhongshu Li|2024|Chemical Science|15|20030|doi:10.1039/D4SC06462C
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.cc2jnyjp
title: CCDC 2343833: Experimental Crystal Structure Determination

description: Related Article: Jieli Lin, Shihua Liu, Shunlin Zheng, Hansjörg Grützmacher, Cheng-Yong Su, Zhongshu Li|2024|Chemical Science|15|20030|doi:10.1039/D4SC06462C
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.c.3643769_d1.v1
title: Additional file 2: Figure S1. of Exploring how individuals complete the choice tasks in a discrete choice experiment: an interview study

description: Example of choice task rotavirus DCE, word document. Figure S2. Example of choice task prostate cancer-screening DCE, word document (ZIP 172 kb)
DOI: 10.5517/ccdc.csd.cc2jttjq
title: CCDC 2348514: Experimental Crystal Structure Determination

description: Related Article: Zhenda Fu, Jianzheng Cheng, Xiao-Xi Li, Xingwei Li, Songjie Yu|2024|Org.Lett.|26|9961|doi:10.1021/acs.orglett.4c03798
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.cc2jttkr
title: CCDC 2348515: Experimental Crystal Structure Determination

description: Related Article: Zhenda Fu, Jianzheng Cheng, Xiao-Xi Li, Xingwei Li, Songjie Yu|2024|Org.Lett.|26|9961|doi:10.1021/acs.orglett.4c03798
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.c.3643793_d14.v1
title: Additional file 8: Table S4. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: Molecular evolution of jiDE genes. (XLSX 61Â kb) (XLSX 62Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d16.v1
title: Additional file 24: Table S14. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: Details of expression quantitative trait loci (eQTLs) detected changed-tissues Minghui63-Zhenshan97 differentially expressed (MZDE) genes. (XLSX 127Â kb) (XLSX 121Â kb)
DOI: 10.15468/dl.ns78q8
title: Occurrence Download

description: A dataset containing 826 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "TaxonKey is Harpia harpyja (Linnaeus, 1758)"
 ]
}

 The dataset includes 826 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037994-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3643793_d20.v1
title: Additional file 17: Table S9. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: GO enrichment analysis of tissue specific changed-tissues jiDE genes of the NM combination. (XLSX 49Â kb) (XLSX 47Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d18.v1
title: Additional file 15: Table S7. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: GO enrichment analysis of global jiDE genes of the NM combination. (XLSX 57Â kb) (XLSX 52Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d22.v1
title: Additional file 5: Table S3. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: Highly expressed genes and the two types of jiDE genes of the two japonica-indica combinations in the five tissues. (XLSX 53Â kb) (XLSX 51Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d26.v1
title: Additional file 20: Table S11. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: Expression types of global DE genes among the three strains. (XLSX 49Â kb) (XLSX 45Â kb)
DOI: 10.6084/m9.figshare.c.3643808_d3.v1
title: Additional file 1: Table S1. of Dynamics of the fecal microbiome in patients with recurrent and nonrecurrent Clostridium difficile infection

description: Sample description and metadata. The relative abundance of the top 100 operational taxonomic units (OTUs), with taxonomic classification, for all samples is listed in columns. Metadata for each sample is described across each row. (XLSX 236 kb)