cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3606836_d17
title: Additional file 1: Table S1. of A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition

description: The BLASTN searching results of 4428 BESs with sweetpotato EST database. (XLS 635 kb)
DOI: 10.6084/m9.figshare.c.3606884_d8
title: Additional file 4: of Low genetic diversity despite multiple introductions of the invasive plant species Impatiens glandulifera in Europe

description: Likelihood values, ΔK values and CLUMPP H values for the different STRUCTURE runs.
DOI: 10.6084/m9.figshare.c.3606836_d18
title: Additional file 13: Table S11. of A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition

description: Paired BESs aligned on the same contigs of Mx23Hm in the correct orientation. (XLS 106 kb)
DOI: 10.6084/m9.figshare.c.3606899_d7
title: Additional file 1: Table S1. of Next-generation sequencing diagnostics of bacteremia in septic patients

description: List of fungal reference genomes included in the kraken database to identify microbial reads in non-human reads. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3606911_d3
title: Additional file 3: Table S3. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

description: Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented Microbispora ATCC-PTA-5024 proteins identified from membrane proteome analysis at A substages. (XLSX 37 kb)
DOI: 10.15468/dl.36b5y7
title: Occurrence Download

description: A dataset containing 295 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is one of (China, Japan, Chinese Taipei)",
 "TaxonKey is Pistia L."
 ]
}

 The dataset includes 295 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032928-241126133413365/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.3606899_d9
title: Additional file 3: Table S6. of Next-generation sequencing diagnostics of bacteremia in septic patients

description: Total read counts per sample and species. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.c.3606911_d4
title: Additional file 8: Table S6. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

description: Numbers of KEGG orthology groups participating in molecular and metabolic processes as inferred from genome and proteome analyses, respectively. (XLS 24 kb)
DOI: 10.6084/m9.figshare.c.3607010_d8
title: Additional file 2: of TNL genes in peach: insights into the post-LRR domain

description: Exon and domain structures of all predicted TNL-related peptides. Exon sizes are shown above the colour shapes reflecting the different domains. (XLSX 115Â kb)
DOI: 10.6084/m9.figshare.c.3607049_d1
title: Additional file 1: of Is multiple nest building an adequate strategy to cope with inter-species nest usurpation?

description: Supplementary material. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.c.3607052_d1
title: Additional file 3: Table S2. of Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops

description: Conserved alternative splicing gene list in rice, sorghum, corn, and Brachypodium distachyon. (XLS 75 kb)
DOI: 10.6084/m9.figshare.c.3607052_d2
title: Additional file 2: Table S3. of Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops

description: Number of conserved alternative splicing genes in cereal crops. (XLS 31 kb)
DOI: 10.15468/dl.5udr6m
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oplophoridae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 23 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032929-241126133413365/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.3607130_d4
title: Additional file 5: of Description of the interaction between Candida albicans and macrophages by mixed and quantitative proteome analysis without isolation

description: Proteins identified in this study for C. albicans monoculture (976 proteins) and macrophage monocultre (1,357 proteins).
DOI: 10.6084/m9.figshare.c.3607133_d6
title: Additional file 5: of Identification of microRNAs regulating Escherichia coli F18 infection in Meishan weaned piglets

description: Potential target genes prediction analysis of differential expressed miRNAs between E. coli F18-resistant and -sensitive groups. (XLSX 2596Â kb)
DOI: 10.6084/m9.figshare.c.3607130_d5
title: Additional file 2: of Description of the interaction between Candida albicans and macrophages by mixed and quantitative proteome analysis without isolation

description: Proteins identified in this study from co-culture of C. albicans (483 proteins) and macrophages (1,253 proteins).
DOI: 10.6084/m9.figshare.c.3607160_d2
title: Additional file 12: Table S7. of A novel approach identifies the first transcriptome networks in bats: a new genetic model for vocal communication

description: FOXP1-target relationships identified in the midnight blue network. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.c.3607160_d3
title: Additional file 9: Table S5. of A novel approach identifies the first transcriptome networks in bats: a new genetic model for vocal communication

description: Full GO for PAG modules (XLSX 83 kb)
DOI: 10.6084/m9.figshare.c.3607130_d7
title: Additional file 1: of Description of the interaction between Candida albicans and macrophages by mixed and quantitative proteome analysis without isolation

description: False positive proteins of C. albicans (18 proteins) and macrophage (30 proteins).
DOI: 10.6084/m9.figshare.c.3607160_d5
title: Additional file 4: Table S2. of A novel approach identifies the first transcriptome networks in bats: a new genetic model for vocal communication

description: Gene ontology of top 500 overexpressed genes for cortex and PAG (XLSX 50 kb)
DOI: 10.6084/m9.figshare.c.3607226_d9
title: Additional file 4: of Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia

description: KEGG and GO enrichment analysis results. This is an “xls” format file that provides enrichment test results from GOStats package for KEGG pathways and GO biological processes for both hyper- and hypo-C-DMRs and DMRs from pooled sample analysis in separate excel sheets, respectively. (XLS 916 kb)
DOI: 10.6084/m9.figshare.c.3607277_d1
title: Additional file 1: of Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model

description: List of the 150 organisms whose genomic sequences were used in our study. (XLSX 69 kb)
DOI: 10.6084/m9.figshare.c.3607286_d1
title: MOESM2 of Deletion of the 2-acyl-glycerophosphoethanolamine cycle improve glucose metabolism in Escherichia coli strains employed for overproduction of aromatic compounds

description: Additional file 2: Table S2. Mutation rates in both evolved strains based on mutation appearance in the rpoB locus. Mutation rates were determined by a modified Luria-Delbrück fluctuation test, employing the MSS-MLE and the LC methods in the estimation of the number of mutants [30–32]. The mutation frequency also was determinated.
DOI: 10.6084/m9.figshare.c.3607286_d2
title: MOESM5 of Deletion of the 2-acyl-glycerophosphoethanolamine cycle improve glucose metabolism in Escherichia coli strains employed for overproduction of aromatic compounds

description: Additional file 5: Table S4. Oligonucleotides employed in this study. This table lists the oligonucleotides utilized in this work. Section A shows the oligonucleotides used for DNA sequencing with the Sanger method, for the gene disruption confirmations generated by Datsenko-Wanner method and the deletion confirmation that occurred in the evolved strains. Section B lists the oligonucleotides utilized for gene disruption with the Datsenko-Wanner methodology. Section C lists the oligonucleotides utilized for RT-qPCR analysis not previously reported.
DOI: 10.6084/m9.figshare.c.3607283_d3
title: Additional file 3: Table S3. of Molecular epidemiology of drug-resistant Neisseria gonorrhoeae in Russia (Current Status, 2015)

description: List of all isolates used in this study with their sequence types, drug resistance profiles and biochip analysis data. (XLSX 21Â kb)
DOI: 10.6084/m9.figshare.c.3607286_d4
title: MOESM4 of Deletion of the 2-acyl-glycerophosphoethanolamine cycle improve glucose metabolism in Escherichia coli strains employed for overproduction of aromatic compounds

description: Additional file 4: Table S3. RT-qPCR mRNA expression values of central carbon metabolism, in the evolved strains. Relative mRNA concentrations of central metabolism and regulatory genes of PB11, PB12 and PB13 strains, grown in glucose as the sole carbon source were determined by RT-qPCR. Most of these values have been previously reported (*) and are presented here for discussion and comparison purposes [2, 9–11]. Data in this table are reported as relative expression levels of the parental strain JM101. The mRNA level of each gene in the parental strain was used as control to normalize the data, assigning it the value of one. N.D. Not determined.
DOI: 10.6084/m9.figshare.c.3607301_d1
title: Additional file 1: Table S1. of Fluorescence activated cell sorting followed by small RNA sequencing reveals stable microRNA expression during cell cycle progression

description: Characterization of cell cycle sorted cells and isolated RNA quantity in various cell types. Purity of cell cycle sort was determined by re-analyzing the sorted populations by FACS analysis: percentage was determined by the portion of cells residing in the gate previously designated for a certain cell cycle phase. Data of four replicate experiments. Data are given as × 1000 cells (sorted cells) and are shown as mean ± standard deviation. Table S2. Name and details of primers used for mRNA and miRNA expression qRT-PCR measurements. mRNA primers (Panel A, cat. No: 4331182) and miRNA primers (Panel B, cat. No: 4427975). All primers were from Applied Biosystems by Life Technologies. Table S3. Normalized expression of differently expressed genes between cell cycle phases in various cell types. Normalized expression of genes with fold change &gt; 2 between cell cycle phases detected in HDFa cells (Panel A). Normalized expression of significantly differently expressed genes in cell cycle phases detected in NCI-H295R (Panel B) and HeLa (Panel C) cells. Note: For Panel B and C, genes are listed in the manner as shown in the heat map (Fig. 2, panel A and B, respectively). Table S4. List of genes shown on Venn diagram (Fig. 3, panel a). Genes are marked with “1” if being found cycling by either method (HDFa SORT, PF synchr, HeLa SORT, HeLa synchr). Gene IDs are Gene Symbols, if available or probe IDs. Table S5. List of HeLa cell cycle genes being present in enriched GO terms. Table 1 presents GO terms which are enriched in gene lists unique to HeLa SORT, HeLa synchronization experiments and the overlap beween HeLa SORT and synchronization lists. Gene symbols of genes being present in the gene lists and the enriched GO terms are shown here (HeLa SORT \ HeLa synchr - Panel A; HeLa synchr \ HeLa SORT – Panel B; HeLa SORT ∩ HeLa synchr – Panel C). (XLS 743 kb)
DOI: 10.6084/m9.figshare.c.3607286_d5
title: MOESM1 of Deletion of the 2-acyl-glycerophosphoethanolamine cycle improve glucose metabolism in Escherichia coli strains employed for overproduction of aromatic compounds

description: Additional file 1: Table S1. This table lists the data provided by Winter Genomics Inc. (WG) obtained from the whole genome sequence of the PB13 strain in comparison to the parental strains JM101 and PB11. Section A includes a list of 13 genes in which, accordingly to this company non-synonymous point mutations occurred changing the coding regions in structural genes. The table also includes (Section B) the list of 8 genes in which synonymous mutations also occurred.
DOI: 10.6084/m9.figshare.c.3607352_d10
title: Additional file 11: of Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design

description: LifeTech NGS ERCC controls data in comma-separated values (CSV) format. (CSV 7Â kb)
DOI: 10.6084/m9.figshare.c.3607364_d7
title: Additional file 7: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

description: Radix mt-genome primers. (XLS 36 kb)
DOI: 10.6084/m9.figshare.c.3607370_d6
title: Additional file 7: of Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis

description: GO and KEGG classes in flower upregulated genes. (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.c.3607352_d11
title: Additional file 8: of Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design

description: NIAID microarray ERCC controls data in comma-separated values (CSV) format. (CSV 15Â kb)
DOI: 10.15468/dl.fktkdm
title: Occurrence Download

description: A dataset containing 149 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Luidiidae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 149 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032930-241126133413365/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.3607352_d12
title: Additional file 9: of Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design

description: Agilent 1-color ERCC controls data in comma-separated values (CSV) format. (CSV 14Â kb)
DOI: 10.6084/m9.figshare.c.3607370_d8
title: Additional file 4: of Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis

description: GO and KEGG classes of Crocus transcripts. (XLSX 18460Â kb)
DOI: 10.6084/m9.figshare.c.3607397_d1
title: Additional file 13: of CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries

description: Supplementary file 1. Perl script generating random sgRNA target sites. (PL 1 kb)
DOI: 10.6084/m9.figshare.c.3607466_d9
title: Additional file 9: of Identification of protein-damaging mutations in 10 swine taste receptors and 191 appetite-reward genes

description: Variant impact and effect classification according to SNPeff. This table describes the types of genetic variants according to their effect on protein sequence. This table has been modified from the SNPeff manual ( http://snpeff.sourceforge.net/SnpEff_manual.html#input ). (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3607433_d18
title: Additional file 15: Table S7. of Population Dynamics Among six Major Groups of the Oryza rufipogon Species Complex, Wild Relative of Cultivated Asian Rice

description: Numeric LD Decay. (XLSX 14Â kb)
DOI: 10.15468/dl.j5ssgf
title: Occurrence Download

description: A dataset containing 6348 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pleurozia Dumort."
 ]
}

 The dataset includes 6348 records from 141 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032931-241126133413365/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.3607517_d1
title: Additional file 1: Figure S1. of DEF6 expression in ovarian carcinoma correlates with poor patient survival

description: Kaplan-Meier curves for overall survival in four histological subtypes of ovarian carcinoma patients according to DEF6, p16 and p53 expressions. A, Patients with high DEF6 expression (scores 2 and 3; n = 60) versus low DEF6 expression (scores 0 and 1; n = 15) in high-grade serous carcinoma. (H: high DEF6 expression; L: low DEF6 expression). B, Patients with high p16 expression (scores 2 and 3; n = 56) versus low p16 expression (scores 0 and 1; n = 18) in high-grade serous carcinoma. (H: high p16 expression; L: low p16 expression). C, Patients with aberrant p53 expression (scores 0 and 3; n = 62) versus insignificant p53 expression (scores 1 and 2; n = 12) in high-grade serous carcinoma. D, Patients with high DEF6 expression (scores 2 and 3; n = 20) versus low DEF6 expression (scores 0 and 1; n = 16) in mucinous carcinoma. (H: high DEF6 expression; L: low DEF6 expression). E, Patients with high p16 expression (scores 2 and 3; n = 32) versus low p16 expression (scores 0 and 1; n = 3) in mucinous carcinoma. (H: high p16 expression; L: low p16 expression). F, Patients with aberrant p53 expression (scores 0 and 3; n = 17) versus insignificant p53 expression (scores 1 and 2; n = 19) in mucinous carcinoma. G, Patients with high DEF6 expression (scores 2 and 3; n = 6) versus low DEF6 expression (scores 0 and 1; n = 22) in endometrioid carcinoma. (H: high DEF6 expression; L: low DEF6 expression). H, Patients with high p16 expression (scores 2 and 3; n = 17) versus low p16 expression (scores 0 and 1; n = 11) in endometrioid carcinoma. (H: high p16 expression; L: low p16 expression). I, Patients with aberrant p53 expression (scores 0 and 3; n = 9) versus insignificant p53 expression (scores 1 and 2; n = 19) in endometrioid carcinoma. J, Patients with high p16 expression (scores 2 and 3; n = 30) versus low p16 expression (scores 0 and 1; n = 11) in clear cell carcinoma. (H: high p16 expression; L: low p16 expression). K, Patients with aberrant p53 expression (scores 0 and 3; n = 10) versus insignificant p53 expression (scores 1 and 2; n = 31) in clear cell carcinoma. (ZIP 195 kb)
DOI: 10.6084/m9.figshare.c.3607535_d1
title: Additional file 3: of A method for identification of highly conserved elements and evolutionary analysis of superphylum Alveolata

description: Presents summary data on the clusters. The Resume sheet provides some information on the algorithm results with different parameters. The variant with the threshold length 65Â bp, which is discussed in the main paper, is highlighted in pink. In lines 15â  42, the number of m-dense clusters and their vertices are shown for m values from 30 to 3. For example (line 15): 14 clusters were found containing words from all 30 genomes; these clusters comprise a total of 3736 vertices, i.e. 9 words per genome on average. Another example (line 35): 84 clusters were found containing words from 10 genomes; 1.2 words per genome on average. On the Clusters sheet, each line starting from the sixth one corresponds to a cluster. Column A contains the cluster number highlighted in the case of untranslated or unknown UCE (similar to Additional file 2). The HCE type is shown in column B as follows: if any of cluster words was found in Rfam, the cluster corresponds to a known RNA such as tRNA, snRNA, etc.; the column contains this RNA label; if any of cluster words overlaps with a CDS, it corresponds to a protein (exon) and is labeled as a protein; if any of cluster words overlaps with a gene, it corresponds to an intron or other untranslated region and is labeled as an intron; otherwise the cluster describes an unknown HCE (no label in column B). Column C shows the total number of words in the cluster; column D, the total number of species containing these words; and columns Eâ  AH, the number of words from each species. (XLSX 1109 kb)
DOI: 10.6084/m9.figshare.c.3607538_d1
title: Additional file 9: of A computationally constructed ceRNA interaction network based on a comparison of the SHEE and SHEEC cell lines

description: KEGG pathway enrichment analysis results of ceRNAs. (XLS 27Â kb)
DOI: 10.15468/dl.kqkh37
title: Occurrence Download

description: A dataset containing 3179 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "GadmGid is one of (IDN.34_1, IDN.34.1.3_1)",
 "IucnRedListCategory is NT",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 3179 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032932-241126133413365/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.3607616_d1
title: Additional file 1: of Changes in global gene expression of Vibrio parahaemolyticus induced by cold- and heat-stress

description: DAVID categories. Additional file includes DAVID data for all temperatures. (XLSX 25Â kb)
DOI: 10.6084/m9.figshare.c.3607607_d5
title: Additional file 4: Table S2. of Construction of possible integrated predictive index based on EGFR and ANXA3 polymorphisms for chemotherapy response in fluoropyrimidine-treated Japanese gastric cancer patients using a bioinformatic method

description: Extracted SNPs with qâ
DOI: 10.6084/m9.figshare.c.3607616_d2
title: Additional file 2: of Changes in global gene expression of Vibrio parahaemolyticus induced by cold- and heat-stress

description: Differentially expressed genes with log 2 fold change &gt;1.5 and adjusted p -value &lt;0.05 in each condition. Additional file includes the homolog and antagonistic reacting genes. (XLSX 192Â kb)
DOI: 10.6084/m9.figshare.c.3607637_d1
title: Additional file 2: of Etoposide damages female germ cells in the developing ovary

description: Full data set for Figures 2-7. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.c.3607643_d1
title: Additional file 3: Table S2. of Functional outcome measures in a surgical model of hip osteoarthritis in dogs

description: Complete dataset of Spearman rank order correlations performed for all outcome measures. Correlations highlighted in red are significant at p&lt;0.05.(XLSX 133 kb)
DOI: 10.15468/dl.xdjgaz
title: Occurrence Download

description: A dataset containing 7219 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Alstonia scholaris (L.) R.Br."
 ]
}

 The dataset includes 7219 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032934-241126133413365/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.3607715_d11
title: MOESM7 of Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type

description: Additional file 7: Tables S1 and S2. S1: Matrix of all correlations with a cut-off of 0.01. S2: Matrix of all correlations with a cut-off of 0.05.
DOI: 10.6084/m9.figshare.c.3607766_d2
title: Additional file 2: of Implementation of Child Death Review in the Netherlands: results of a pilot study

description: Form C - Analysis Proforma. (ODT 32 kb)
DOI: 10.6084/m9.figshare.c.3607715_d12
title: MOESM23 of Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type

description: Additional file 23. Calculations sheet for richness and evenness.