cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11999130
title: Additional file 1 of SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework

description: Additional file 1 Source code and sample data for SEQing. The Python code and samples of Arabidopsis thaliana iCLIP (GSE99427) and RNA-seq (GSE99615) data used to start the sample dataset dashboard.
DOI: 10.6084/m9.figshare.11999130.v1
title: Additional file 1 of SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework

description: Additional file 1 Source code and sample data for SEQing. The Python code and samples of Arabidopsis thaliana iCLIP (GSE99427) and RNA-seq (GSE99615) data used to start the sample dataset dashboard.
DOI: 10.6084/m9.figshare.11999109
title: Additional file 9 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

description: Additional file 9. Enriched gene ontology (GO) terms for transcripts associated by Pearson correlation to traits Tuber Blight Score (TBS), Alternaria infection volume (AIV), Number of Tubers (NoT), Height (H) and Growth Rate (GR).
DOI: 10.6084/m9.figshare.11999109.v1
title: Additional file 9 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

description: Additional file 9. Enriched gene ontology (GO) terms for transcripts associated by Pearson correlation to traits Tuber Blight Score (TBS), Alternaria infection volume (AIV), Number of Tubers (NoT), Height (H) and Growth Rate (GR).
DOI: 10.6084/m9.figshare.11999085
title: Additional file 6 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

description: Additional file 6. Top 20 positively and negatively associated transcripts for each trait (Table S8) and transcripts with annotations and Pearson (PCC) and Spearman (SCC) correlations (Table S9).
DOI: 10.6084/m9.figshare.11999073
title: Additional file 5 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

description: Additional file 5. Differentially expressed genes comparing progeny lines resistant and susceptible to P. infestans (p 2; Table S7).
DOI: 10.6084/m9.figshare.11999085.v1
title: Additional file 6 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

description: Additional file 6. Top 20 positively and negatively associated transcripts for each trait (Table S8) and transcripts with annotations and Pearson (PCC) and Spearman (SCC) correlations (Table S9).
DOI: 10.6084/m9.figshare.11999073.v1
title: Additional file 5 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

description: Additional file 5. Differentially expressed genes comparing progeny lines resistant and susceptible to P. infestans (p 2; Table S7).
DOI: 10.6084/m9.figshare.11999058
title: Additional file 3 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

description: Additional file 3. Expression values of transcripts in all progeny lines and the two parents (Table S5) and differentially expressed genes between progeny lines and parents (Table S6).
DOI: 10.6084/m9.figshare.11999058.v1
title: Additional file 3 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

description: Additional file 3. Expression values of transcripts in all progeny lines and the two parents (Table S5) and differentially expressed genes between progeny lines and parents (Table S6).
DOI: 10.6084/m9.figshare.11999052
title: Additional file 2 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

description: Additional file 2. Evaluation of master transcriptome assembly by re-mapping sequencing reads by bowtie2 aligner (Table S2) and estimation of sequence completion by BUSCO (Table S3) as well as annotations by Uniprot, ITAG, PGSC and Gene Ontology (GO) of identified transcripts (Table S4).
DOI: 10.6084/m9.figshare.11999049
title: Additional file 1 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

description: Additional file 1. Values including means of traits used for transcript association analysis (Table S1). NA denotes missing values.
DOI: 10.6084/m9.figshare.11999049.v1
title: Additional file 1 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

description: Additional file 1. Values including means of traits used for transcript association analysis (Table S1). NA denotes missing values.
DOI: 10.6084/m9.figshare.11999052.v1
title: Additional file 2 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

description: Additional file 2. Evaluation of master transcriptome assembly by re-mapping sequencing reads by bowtie2 aligner (Table S2) and estimation of sequence completion by BUSCO (Table S3) as well as annotations by Uniprot, ITAG, PGSC and Gene Ontology (GO) of identified transcripts (Table S4).
DOI: 10.6084/m9.figshare.11999043
title: Additional file 11 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

description: Additional file 11. Primer sequences for qPCR targets.
DOI: 10.6084/m9.figshare.11999043.v1
title: Additional file 11 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

description: Additional file 11. Primer sequences for qPCR targets.
DOI: 10.15468/ka64rq
title: Pseudeburia, a New South American genus of longhorned beetle (Cerambycidae: Cerambycinae: Bothriospilini)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Botero, Juan Pablo (2015): Pseudeburia, a New South American genus of longhorned beetle (Cerambycidae: Cerambycinae: Bothriospilini). Journal of Natural History 49 (41): 2583-2587, DOI: 10.1080/00222933.2015.1038328
DOI: 10.6084/m9.figshare.11998629
title: Additional file 3 of AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species

description: Additional file 3. Result figures enrichment analysis in case study 2.
DOI: 10.6084/m9.figshare.11998629.v1
title: Additional file 3 of AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species

description: Additional file 3. Result figures enrichment analysis in case study 2.
DOI: 10.6084/m9.figshare.11998620
title: Additional file 1 of AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species

description: Additional file 1. Result tables enrichment analysis in case study 1.
DOI: 10.6084/m9.figshare.11998620.v1
title: Additional file 1 of AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species

description: Additional file 1. Result tables enrichment analysis in case study 1.
DOI: 10.6084/m9.figshare.11998608
title: Additional file 8 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

description: Additional file 8 Table S5. GO terms analysis of PQS-associated genes for Laverania, rodent, and avian malaria parasites. Lists of PQS-associated genes for each species were analyzed for gene ontology (GO) terms in PlasmoDB. The table shows overrepresented GO terms for molecular function and biological processes for each species, as well as binning assignments that were used for the construction of the heat maps in Fig. 7.
DOI: 10.6084/m9.figshare.11998608.v1
title: Additional file 8 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

description: Additional file 8 Table S5. GO terms analysis of PQS-associated genes for Laverania, rodent, and avian malaria parasites. Lists of PQS-associated genes for each species were analyzed for gene ontology (GO) terms in PlasmoDB. The table shows overrepresented GO terms for molecular function and biological processes for each species, as well as binning assignments that were used for the construction of the heat maps in Fig. 7.
DOI: 10.6084/m9.figshare.11998593
title: Additional file 6 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

description: Additional file 6 Table S4. Associations between PQSs and variantly-expressed multigene families besides var in Laveranian genomes. Numbers and proportions of genes in non-var variantly-expressed multigene families that contain at least one PQS, in Laveranian species. Copy numbers of genes in each family were found in PlasmoDB.
DOI: 10.6084/m9.figshare.11998593.v1
title: Additional file 6 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

description: Additional file 6 Table S4. Associations between PQSs and variantly-expressed multigene families besides var in Laveranian genomes. Numbers and proportions of genes in non-var variantly-expressed multigene families that contain at least one PQS, in Laveranian species. Copy numbers of genes in each family were found in PlasmoDB.
DOI: 10.6084/m9.figshare.11998581
title: Additional file 3 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

description: Additional file 3 Table S3. Co-distribution of PQSs with variantly-expressed multigene families in Laverania, rodent, and avian malaria parasites. For each genome, the mean distance between var or pir genes and their nearest PQS was compared to the mean distance in a simulated genome where var or pir genes occurred at random. Differences between the actual and simulated datasets were assessed by Welch’s t-test, two-tailed.
DOI: 10.6084/m9.figshare.11998575
title: Additional file 2 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

description: Additional file 2 Table S2. Comparison of total PQSs and var-associated PQSs in Laveranian genomes. PQSs were considered “var-associated” if they were found within a var coding sequence, or if the nearest gene, within 2 kbp, was a var gene. Copy numbers of var genes were found in PlasmoDB. Telomeric-PQSs were excluded.
DOI: 10.6084/m9.figshare.11998569
title: Additional file 4 of Cloacal swabs and alcohol bird specimens are good proxies for compositional analyses of gut microbial communities of Great tits (Parus major)

description: Additional file 4: Table S5. Results from the DeSeq2 analysis on differentially abundant bacterial genera between fresh and differently aged alcohol specimens. Each tab includes data from one region of the digestive tract.
DOI: 10.6084/m9.figshare.11998575.v1
title: Additional file 2 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

description: Additional file 2 Table S2. Comparison of total PQSs and var-associated PQSs in Laveranian genomes. PQSs were considered “var-associated” if they were found within a var coding sequence, or if the nearest gene, within 2 kbp, was a var gene. Copy numbers of var genes were found in PlasmoDB. Telomeric-PQSs were excluded.
DOI: 10.6084/m9.figshare.11998581.v1
title: Additional file 3 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

description: Additional file 3 Table S3. Co-distribution of PQSs with variantly-expressed multigene families in Laverania, rodent, and avian malaria parasites. For each genome, the mean distance between var or pir genes and their nearest PQS was compared to the mean distance in a simulated genome where var or pir genes occurred at random. Differences between the actual and simulated datasets were assessed by Welch’s t-test, two-tailed.
DOI: 10.6084/m9.figshare.11998566
title: Additional file 13 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

description: Additional file 13 Table S8. Putative G-quadruplex-forming sequences in the genomes of Plasmodium parasites, found by G4 Hunter. Genomes were downloaded from PlasmoDB, v. 44, and searched using G4 Hunter with the parameters: threshold: 1.7, window size: 25, csv data: grouped. An additional search of the P. falciparum genome was also conducted at a lower threshold of 1.25. As per the G4 Hunter algorithm, PQSs on the reverse complement sequence had negative scores, and all locations were reported relative to the 5′ end of the sense strand. The “Strand (cf gene or nearest gene)” category was denoted as antisense if the PQS was on the opposite strand of its nearest gene, or sense if the PQS was on the same strand as its nearest gene. The “distance from nearest gene” was positive if the PQS was upstream of the nearest gene, negative if the PQS was downstream of the nearest gene, or equal to 0 if the PQS was in the coding sequence of the nearest gene.
DOI: 10.6084/m9.figshare.11998572
title: Additional file 1 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

description: Additional file 1 Table S1. Genome sizes and G/C content of Plasmodium parasites. Genome sequences were downloaded from PlasmoDB v. 44. Genome sizes and G/C contents were calculated using custom code. Custom code was used to parse the coding sequences for var genes and to calculate their associated G/C contents.
DOI: 10.6084/m9.figshare.11998572.v1
title: Additional file 1 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

description: Additional file 1 Table S1. Genome sizes and G/C content of Plasmodium parasites. Genome sequences were downloaded from PlasmoDB v. 44. Genome sizes and G/C contents were calculated using custom code. Custom code was used to parse the coding sequences for var genes and to calculate their associated G/C contents.
DOI: 10.6084/m9.figshare.11998566.v1
title: Additional file 13 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

description: Additional file 13 Table S8. Putative G-quadruplex-forming sequences in the genomes of Plasmodium parasites, found by G4 Hunter. Genomes were downloaded from PlasmoDB, v. 44, and searched using G4 Hunter with the parameters: threshold: 1.7, window size: 25, csv data: grouped. An additional search of the P. falciparum genome was also conducted at a lower threshold of 1.25. As per the G4 Hunter algorithm, PQSs on the reverse complement sequence had negative scores, and all locations were reported relative to the 5′ end of the sense strand. The “Strand (cf gene or nearest gene)” category was denoted as antisense if the PQS was on the opposite strand of its nearest gene, or sense if the PQS was on the same strand as its nearest gene. The “distance from nearest gene” was positive if the PQS was upstream of the nearest gene, negative if the PQS was downstream of the nearest gene, or equal to 0 if the PQS was in the coding sequence of the nearest gene.
DOI: 10.6084/m9.figshare.11998569.v1
title: Additional file 4 of Cloacal swabs and alcohol bird specimens are good proxies for compositional analyses of gut microbial communities of Great tits (Parus major)

description: Additional file 4: Table S5. Results from the DeSeq2 analysis on differentially abundant bacterial genera between fresh and differently aged alcohol specimens. Each tab includes data from one region of the digestive tract.
DOI: 10.6084/m9.figshare.11998560
title: Additional file 12 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

description: Additional file 12 Table S7. Putative G-quadruplex-forming sequences in the genomes of Plasmodium parasites, found by QGRS Mapper. Genomes were downloaded from PlasmoDB, v. 44, and searched using QGRS Mapper with the parameters: regex: G3N(0 − 11)G3N(0 − 11)G3N(0 − 11)G3, max length: 45, min G-group: 3, loop size: 0–11. “RC_Location Calculated” refers to the location of PQSs on the antisense strand, relative to the 5′ end of the sense strand. The “Strand (cf gene or nearest gene)” category was denoted as antisense if the PQS was on the opposite strand of its nearest gene, or sense if the PQS was on the same strand as its nearest gene. The “distance from nearest gene” was positive if the PQS was upstream of the nearest gene, negative if the PQS was downstream of the nearest gene, or equal to 0 if the PQS was in the coding sequence of the nearest gene.
DOI: 10.6084/m9.figshare.11998554
title: Additional file 11 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

description: Additional file 11 Table S6. Comparison of QGRS Mapper and G4 Hunter with experimental G4-seq data. The in silico predictions by QGRS Mapper and G4 Hunter were compared to experimental G4-seq data [29] by searching for instances where PQS start/end locations overlapped with G4-seq window locations. The table shows PQS sites and indicates whether they were found within a G4-seq window.
DOI: 10.6084/m9.figshare.11998560.v1
title: Additional file 12 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

description: Additional file 12 Table S7. Putative G-quadruplex-forming sequences in the genomes of Plasmodium parasites, found by QGRS Mapper. Genomes were downloaded from PlasmoDB, v. 44, and searched using QGRS Mapper with the parameters: regex: G3N(0 − 11)G3N(0 − 11)G3N(0 − 11)G3, max length: 45, min G-group: 3, loop size: 0–11. “RC_Location Calculated” refers to the location of PQSs on the antisense strand, relative to the 5′ end of the sense strand. The “Strand (cf gene or nearest gene)” category was denoted as antisense if the PQS was on the opposite strand of its nearest gene, or sense if the PQS was on the same strand as its nearest gene. The “distance from nearest gene” was positive if the PQS was upstream of the nearest gene, negative if the PQS was downstream of the nearest gene, or equal to 0 if the PQS was in the coding sequence of the nearest gene.
DOI: 10.6084/m9.figshare.11998548
title: Additional file 1 of Cloacal swabs and alcohol bird specimens are good proxies for compositional analyses of gut microbial communities of Great tits (Parus major)

description: Additional file 1: Table S1. OTU table of all samples, categorized according to the sample region and preservation method (freshly dissected, two-weeks old and two-month alcohol specimens).
DOI: 10.6084/m9.figshare.11998554.v1
title: Additional file 11 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

description: Additional file 11 Table S6. Comparison of QGRS Mapper and G4 Hunter with experimental G4-seq data. The in silico predictions by QGRS Mapper and G4 Hunter were compared to experimental G4-seq data [29] by searching for instances where PQS start/end locations overlapped with G4-seq window locations. The table shows PQS sites and indicates whether they were found within a G4-seq window.
DOI: 10.6084/m9.figshare.11998548.v1
title: Additional file 1 of Cloacal swabs and alcohol bird specimens are good proxies for compositional analyses of gut microbial communities of Great tits (Parus major)

description: Additional file 1: Table S1. OTU table of all samples, categorized according to the sample region and preservation method (freshly dissected, two-weeks old and two-month alcohol specimens).
DOI: 10.6084/m9.figshare.11998512
title: Additional file 1 of Research methodology used in the 50 most cited articles in the field of pediatrics: types of studies that become citation classics

description: Additional file 1. Supplementary file 1. Data for all characteristics of pediatrics’ citation classics that were analyzed within the study. The Excel table contains Supplementary file 1, with all data about characteristics of the 50 highest-cited articles in the field of pediatrics. The Excel table contains the following columns: name of the first author, country of authors’ affiliation, year of publication, years passed since publication, title, times cited in all databases, citation density, Journal Impact Factor for year 2016, Web of Science category, research area, funding source, study design, number of authors.
DOI: 10.6084/m9.figshare.11998512.v1
title: Additional file 1 of Research methodology used in the 50 most cited articles in the field of pediatrics: types of studies that become citation classics

description: Additional file 1. Supplementary file 1. Data for all characteristics of pediatrics’ citation classics that were analyzed within the study. The Excel table contains Supplementary file 1, with all data about characteristics of the 50 highest-cited articles in the field of pediatrics. The Excel table contains the following columns: name of the first author, country of authors’ affiliation, year of publication, years passed since publication, title, times cited in all databases, citation density, Journal Impact Factor for year 2016, Web of Science category, research area, funding source, study design, number of authors.
DOI: 10.15468/jfgwep
title: Muhaka icipe, an enigmatic new genus and species of Kleidotomini (Hymenoptera: Figitidae: Eucoilinae) from an East African coastal forest

description: This dataset contains the digitized treatments in Plazi based on the original journal article Buffington, M. L., Copeland, R. S. (2015): Muhaka icipe, an enigmatic new genus and species of Kleidotomini (Hymenoptera: Figitidae: Eucoilinae) from an East African coastal forest. Journal of Natural History 49 (43): 2597-2607, DOI: 10.1080/00222933.2015.1042411
DOI: 10.6084/m9.figshare.11998494
title: Additional file 1 of Energy efficiency trade-offs in small to large electric vehicles

description: Additional file 1: Table S1. Data of vehicle attributes.
DOI: 10.6084/m9.figshare.11998410
title: Additional file 1 of Bacterial otitis media in sub-Saharan Africa: a systematic review and meta-analysis

description: Additional file 1:Data extraction and summary sheet. Sheet 1 (character): participant information and culture positive rate of Otitis media. Sheet 2 (isolates): Bacterial isolates from Otitis media. Sheet 3 (susceptibility): Drug susceptibility test of isolates.
DOI: 10.6084/m9.figshare.11998410.v1
title: Additional file 1 of Bacterial otitis media in sub-Saharan Africa: a systematic review and meta-analysis

description: Additional file 1:Data extraction and summary sheet. Sheet 1 (character): participant information and culture positive rate of Otitis media. Sheet 2 (isolates): Bacterial isolates from Otitis media. Sheet 3 (susceptibility): Drug susceptibility test of isolates.
DOI: 10.6084/m9.figshare.11997987
title: Supporting data for MBC/SOC at various altitudes of Hyperalic Alisol in Amazon region of Ecuador

description: Data includes results: SOC, MBC, MBC/SOC, humus% at different altitudes.
DOI: 10.6084/m9.figshare.11997969
title: Transmissibility of COVID-19 and its association with temperature and humidity

description: These are the corresponding data in the research article:Xiao-Jing Guo, Hui Zhang, Yi-Ping Zeng et al. Transmissibility of COVID-19 and its association with temperature and humidity, 17 March 2020, PREPRINT (Version 1) available at Research Square [+https://doi.org/10.21203/rs.3.rs-17715/v1+]"R0calculation.xlsx" contains the calculation results of the basic reproduction number R<sub>0</sub> from January 24, 2020 to February 13, 2020 in 11 major cities in China."R0TemperatureHumidity.xlsx" contains the basic reproduction number, temperature and humidity from January 24, 2020 to February 13, 2020 in 4 major cities in China.More details can be seen in the article.
DOI: 10.6084/m9.figshare.11997987.v1
title: Supporting data for MBC/SOC at various altitudes of Hyperalic Alisol in Amazon region of Ecuador

description: Data includes results: SOC, MBC, MBC/SOC, humus% at different altitudes.