cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3625721_d3
title: Additional file 3: Text S1. of Diversity and distribution of alpha satellite DNA in the genome of an Old World monkey: Cercopithecus solatus

description: Alignment used to generate the phylogenetic tree from Fig. 7a. (TXT 28 kb)
DOI: 10.6084/m9.figshare.c.3625730_d5
title: Additional file 1: of Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

description: Proteins encoded by each of the 205 genomes that match the profile HMMs for Tss, Tag, TetR, Rhs, PAAR and PAAR-Rhs proteins. (XLSX 359Â kb)
DOI: 10.6084/m9.figshare.c.3625733_d4
title: Additional file 8: Table S7. of Short chain acyl-CoA dehydrogenase deficiency and short-term high-fat diet perturb mitochondrial energy metabolism and transcriptional control of lipid-handling in liver

description: Predicted activation/inhibition of upstream regulators all categories. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3625745_d4
title: Additional file 3: of An efficient algorithm for identifying primary phenotype attractors of a large-scale Boolean network

description: Attractors for apoptosis in the Mitogen-activated protein kinase (MAPK) model. (XLSX 47Â kb)
DOI: 10.6084/m9.figshare.c.3625940_d3
title: Additional file 5: of 
                     ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining

description: Functional annotation for the pattern. Table S1. Functional enrichment analysis for the promoter pattern. Table S2. Functional enrichment analysis for the gene body pattern. Table S3. Functional enrichment analysis for differentially expressed genes. (XLS 168 kb)
DOI: 10.6084/m9.figshare.c.3625955_d1
title: Additional file 2: of Shedding light on the performance of a pyrosequencing assay for drug-resistant tuberculosis diagnosis

description: Pyrosequencing (PSQ) Performance Dataset. (TXT 400 kb)
DOI: 10.6084/m9.figshare.c.3625940_d4
title: Additional file 1: of 
                     ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining

description: Association rules. A set of all association rules discovered for promoters and gene bodies present and rules are sorted by lift and support. Table S1. All association rules discovered in promoters. Table S2. All association rules discovered in gene bodies. Table S3. mRNA IDs in P155. Table S4. mRNA IDs in G155. Table S5. Pattern Specification. Table S6. Supersets of G155. Table S7. Filtered rules for P155. Table S8. Filtered rules for G155. (XLSX 310 kb)
DOI: 10.6084/m9.figshare.c.3625946_d3
title: Additional file 5: Table S5. of Insights into transcriptional changes that accompany organelle sequestration from the stolen nucleus of Mesodinium rubrum

description: Description and classification of DESeq log2FC under-expressed genes in KN. Genes of note are in bold with parenthetical notation indicating the pathway to which they belong. Genes were assigned to their structural or enzymatic function (for example, “Chromosome”, “Cytoskeleton Proteins”, “Peptidases”, and “Ubiquitin System”) when they returned associations with categories not relevant to this system (for example, Human Diseases and Organismal Processes). (XLSX 48 kb)
DOI: 10.6084/m9.figshare.c.3625946_d4
title: Additional file 1: Table S1. of Insights into transcriptional changes that accompany organelle sequestration from the stolen nucleus of Mesodinium rubrum

description: KEGG Categories evaluated under protein and read count tests. 1. Metabolism, 2. Genetic information Processing, 3. Environmental information processing, and 4. Cellular Processes represent broad KEGG categories. Subcategories in bold (1.0â  4.3) were subject to protein count analyses while italicized pathways within these subcateogries were analyzed by the read count method. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3625955_d3
title: Additional file 3: of Shedding light on the performance of a pyrosequencing assay for drug-resistant tuberculosis diagnosis

description: Pyrosequencing (PSQ) Technical Dataset. (CSV 303 kb)
DOI: 10.6084/m9.figshare.c.3625946_d5
title: Additional file 3: Table S3. of Insights into transcriptional changes that accompany organelle sequestration from the stolen nucleus of Mesodinium rubrum

description: Differential expression of KEGG pathways between GC and KN. GC and KN, mean expression values associated with each pathway calculated from the total number of reads per base pair (normalized read counts for each gene); P adj., P value as determined from Mann-Whitney tests and adjusted with a Benjamini and Hochberg false discovery rateâ
DOI: 10.6084/m9.figshare.c.3626195_d2
title: Additional file 2: of End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis

description: DNAConstructor scripts.zip. Zip file containing files gfp_DNAConstructor.txt and rfp_DNAConstructor.txt, input script files for DNA Constructor. (ZIP 1.7 kb)
DOI: 10.6084/m9.figshare.c.3626207_d1
title: Additional file 1: Table S1. of Explorations to improve the completeness of exome sequencing

description: Coverage of exons in 54 probands. Table S2. Genes with low coverage exons in all 54 probands. (XLSX 9613 kb)
DOI: 10.6084/m9.figshare.c.3626213_d2
title: Additional file 1: of Randomized evaluation and cost-effectiveness of HIV and sexual and reproductive health service referral and linkage models in Zambia

description: De-identified REACH Study Data. This file contains study data, including de-identified data from the client information and tracking registry, the baseline interview, the six-week interview and the six-month interview. (CSV 8081Â kb)
DOI: 10.6084/m9.figshare.c.3626243_d1
title: Additional file 1: of Merozoite surface protein-1 genetic diversity in Plasmodium malariae and Plasmodium brasilianum from Brazil

description: Pairwise similarity matrix among P. malariae/P. brasilianum isolates based on the MSP1 protein sequence fragments. The matrices on the left show, for each fragment separately, the raw numbers of identical amino acids and total amino acids compared between each pair of isolates. The matrices on the right show the aggregated similarity or difference values for the concatenated regions.(XLS 40 kb)
DOI: 10.6084/m9.figshare.c.3626252_d11
title: Additional file 2: Table S2. of Mycoplasma non-coding RNA: identification of small RNAs and targets

description: Mycoplasma hyopneumoniae sRNAs sequence and features predicted. (XLSX 15Â kb)
DOI: 10.15468/dl.emgscz
title: Occurrence Download

description: A dataset listing the 33 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "Geometry POLYGON((-5.525877790051226 36.15737531048895,-5.514811773348711 36.15737531048895,-5.514811773348711 36.168441327191466,-5.525877790051226 36.168441327191466,-5.525877790051226 36.15737531048895))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 33 records were derived from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033934-241126133413365/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.3626441_d12
title: Additional file 8: of Predicting the geographical distributions of the macaque hosts and mosquito vectors of Plasmodium knowlesi malaria in forested and non-forested areas

description: Macaca nemestrina data. Each record of M. nemestrina occurrence is provided with a location and date. Duplicate records within a calendar year have been removed. Locations are classed as points (defined as &lt;25Â km2) or polygons (defined as &gt;25Â km2). (XLSX 130Â kb)
DOI: 10.6084/m9.figshare.c.3626471_d1
title: Additional file 4: of Comparative genomics of Beauveria bassiana: uncovering signatures of virulence against mosquitoes

description: Summary of the unique genes of Bb8028 that were highly expressed in the infected mosquito library. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3626711_d4
title: MOESM3 of Significant geographical differences in prevalence of mutations associated with Plasmodium falciparum and Plasmodium 
                     vivax drug resistance in two regions from Papua New Guinea

description: Additional file 3: Table S3. Pfdhfr, pfdhps, pfcrt and pfmdr1 genotypes prevalence in all P. falciparum infections.
DOI: 10.6084/m9.figshare.c.3626699_d9
title: Additional file 8: of Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species

description: Processed CentriMo results. Significant results from the CentriMo analysis in an alternative format. (XLS 70Â kb)
DOI: 10.6084/m9.figshare.c.3626699_d10
title: Additional file 9: of Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species

description: Windowed FIMO results. Processed results of FIMO analysis with 1Â kb windows. (XLS 39Â kb)
DOI: 10.6084/m9.figshare.c.3626738_d3
title: Additional file 4: of How to assess intra- and inter-observer agreement with quantitative PET using variance component analysis: a proposal for standardisation

description: Raw data of study 2. (CSV 2Â kb)
DOI: 10.15468/dl.jm4xu9
title: Occurrence Download

description: A dataset containing 508 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((8.93669 42.25297,8.94355 42.25297,8.94355 42.25795,8.93669 42.25795,8.93669 42.25297))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 508 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033936-241126133413365/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.3627008_d1
title: Additional file 2: of The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype

description: A: Differential gene expression analysis with polysomal RNAseq. Cuffdiff summary including fold change and test statics of genes found to be differentially expressed within the polysomal RNAseq. B: Differential gene expression analysis with total RNAseq (for explanation see legend to File A). (ZIP 1789 kb)
DOI: 10.6084/m9.figshare.c.3626987_d5
title: Additional file 4: of Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

description: In this file we list the genome-wide in vivo NEUROD2 target genes. (XLSX 799 kb)
DOI: 10.6084/m9.figshare.c.3627005_d2
title: Additional file 2: Figure S1. of Initiation of recombination suppression and PAR formation during the early stages of neo-sex chromosome differentiation in the Okinawa spiny rat, Tokudaia muenninki

description: Frequency distribution of relative rates of A/T → G/C and G/C → A/T substitutions in T. muenninki, mouse, and rat. Each relative rate was estimated from the combined sequences of coding (3rd codon only) and noncoding sites of each gene located on the peritelomeric (a) and pericentromeric (b) regions of T. muenninki neo-sex chromosomes and the corresponding autosomal regions of mouse and rat. The horizontal axis shows the log of the ratio of A/T → G/C substitutions to G/C → A/T substitutions, and the vertical axis shows the number of genes. Black bar: T. muenninki; white bar: M. musculus; and gray bar: R. norvegicus. Figure S2. Comparison of nucleotide sequences of TXNDC11 between T. muenninki neo-X and neo-Y. Single base insertion site in neo-Y–linked sequence was indicated by gray box. The sequences were partially skipped in TMU (2407 bp) and MMU (2410 bp), and the skipped site is shown by double slashes. The accession number for Txndc11 gene from mouse is NM_029582. TMU: T. muenniniki, MMU: M.musculus. Figure S3. The estimation of nucleotide substitution directions in the three species by the maximum parsimony principle. TMU: T. muenninki, MMU: M. musculus, RNO: R. norvegicus. (ZIP 342 kb)
DOI: 10.6084/m9.figshare.c.3626939_d15
title: MOESM15 of Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing

description: Additional file 15. Genes that fail to establish silencing upon Setdb1 depletion. The SNPs that show a failure to establish silencing at day 5 of differentiation in replicates 1 and 2 from RNA-seq in differentiating ES cells are shown. The genes that overlap between replicates 1 and 2 are also shown and the Xi/Xa read count ratio is given.
DOI: 10.6084/m9.figshare.c.3627008_d2
title: Additional file 6: of The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype

description: Parameters employed for the read alignments using Tophat and Cuffdiff. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3626987_d6
title: Additional file 5: of Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

description: Confirmation of NEUROD2 binding to putative target genes identified by the ClosesetGene method. NEUROD2 ChIP and GFP ChIP DNA were used as templates for qPCR analysis. Data is represented as the amount of enrichment in target genes in NEUROD2 ChIP DNA as compared to a negative control GFP ChIP DNA. NEUROD2 non-target genes did not display a significant level of NEUROD2 binding. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3627005_d3
title: Additional file 1: Table S1. of Initiation of recombination suppression and PAR formation during the early stages of neo-sex chromosome differentiation in the Okinawa spiny rat, Tokudaia muenninki

description: List of BAC clones screened for FISH analysis in this study. Table S2. List of genes located on the three regions of neo-sex chromosomes in T. muenninki. Table S3. Comparison of G + C content and nucleotide substitution frequency in three regions among T. muenninki, mouse, and rat with guinea pig as outgroup. Table S4. Frequencies (%) of nucleotide substitutions in sites preceded by C or followed by G in T. muenninki neo-sex chromosomal segments and their autosomal homologs in mouse and rat. Table S5. Detection of male-specific substitutions in 24 genes located on the neo-sex chromosomes. Table S6. Male-specific substitutions observed in the pericentromeric region of the T. muenninki neo-Y chromosome. Table S7. Resulti of tests of the differences in dN/dS ratios among T. muenninki neo-X, neo-Y, and other branches. Table S8. G + C content and frequency of nucleotide substitutions in T. muenninki neo-sex chromosomes and their homologous region in mouse. Table S9. List of BAC clones identified for neo-sex sequence determination. Table S10. Results of next-generation sequencing on an Illumina HiSeq, using a 100 bp paired-end protocol and de novo assembly. Table S11. Results of next-generation sequencing on an Illumina MiSeq, using a 300 bp paired-end protocol and de novo assembly. (ZIP 110 kb)
DOI: 10.6084/m9.figshare.c.3627008_d3
title: Additional file 4: of The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype

description: Total RNAseq FPKM of regulated TSS. Expression levels as measured by total RNAseq of primary transcripts (those containing the same TSS) of genes found to have altered promoter usage between MCF10A and MCF7. The average level of expression (“_FPKM”) as well as the lower (“_conf_lo”) and upper (“_conf_hi”) 95 % confidence intervals are recorded for every primary transcript of each gene. (XLSX 53 kb)
DOI: 10.6084/m9.figshare.c.3626987_d7
title: Additional file 3: of Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

description: In this file we list the genome-wide in vivo NEUROD2 peak coordinates. (XLSX 3195 kb)
DOI: 10.6084/m9.figshare.c.3626987_d8
title: Additional file 9: of Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

description: This table lists the sequences of all primers used in this study. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3627008_d4
title: Additional file 5: of The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype

description: Polysomal RNAseq FPKM of regulated TSS. Expression levels as measured by polysomal RNAseq of primary transcripts (those containing the same TSS) of genes found to have altered promoter usage between MCF10A and MCF7 cells. For an explanation see legend to Additional file 4. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.c.3627266_d1
title: Additional file 1: of Magnetic resonance imaging anatomy of the rabbit brain at 3 T

description: 1. Complete image series of a transverse TSE T2w sequence in one rabbit. 2. Complete image series of a sagittal TSE T2w sequence in the same rabbit as in Additional file 1: 1. 3. Complete image series of a dorsal TSE T2w sequence in the same rabbit as in Additional file 1: 1. 4. Complete image series of a FLAIR longTR CLEAR sequence in the same rabbit as in Additional file 1: 1. 5. Complete image series of a precontrast T1w 3D (TFE SENSE) sequence in the same rabbit as in Additional file 1: 1. 6. Complete image series of a postcontrast T1w 3D (TFE SENSE) sequence in the same rabbit as in Additional file 1: 1.
DOI: 10.6084/m9.figshare.c.3627248_d5
title: Additional file 4: Table S2. of Within-pair differences of DNA methylation levels between monozygotic twins are different between male and female pairs

description: Results of statistical test comparing within-pair difference of methylation levels (WPDMs) between older male and female twin pairs. WPDMs in the male pairs were higher in 11027 CpG islands (10975 were autosomal and 52 were X chromosome), whereas those in female pairs were higher in the other 434 islands (51 were autosomal and 383 were X chromosome). (XLSX 1758 kb)
DOI: 10.6084/m9.figshare.c.3627302_d2
title: Additional file 2: Table S1. of Infectious hematopoietic necrosis virus (IHNV) persistence in Sockeye Salmon: influence on brain transcriptome and subsequent response to the viral mimic poly(I:C)

description: Complete list of significantly differentially expressed probes that were affected by IHNV status (survivor, carrier), poly(I:C)-injection and an interaction effect of both factors.
DOI: 10.15468/dl.h9hjz9
title: Occurrence Download

description: A dataset containing 840 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((10.524 61.64965,12.66984 61.72751,12.60645 62.67834,10.54245 62.67784,10.524 61.64965))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Ovibos moschatus (Zimmermann, 1780), Carnivora, Rangifer tarandus (Linnaeus, 1758), Alces alces (Linnaeus, 1758), Castor fiber Linnaeus, 1758)",
 "Year 2021-2024"
 ]
}

 The dataset includes 840 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033937-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tb78eq
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Sonidos de la Ecoreserva Campo Rubiales (Puerto Gaitán, Meta) - Proyecto FIBRAS"
 ]
}

 The dataset includes 99 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033938-241126133413365/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.3627527_d2
title: Additional file 2 of Design of trials for interrupting the transmission of endemic pathogens

description: Documented R code for simulating trials analogous to the example given in the text. (R 676 kb)
DOI: 10.6084/m9.figshare.c.3627509_d6
title: Additional file 2: Table S1. of Modulation of the human gut microbiota by dietary fibres occurs at the species level

description: Proportional abundance of each operational taxonomic unit (OTU; in %) per sample (97 % OTU cut-off). (XLSX 1538 kb)
DOI: 10.6084/m9.figshare.c.3627530_d2
title: Additional file 2: of Molecular characterization of irinotecan (SN-38) resistant human breast cancer cell lines

description: 32 genes that are differentially expressed in both the MDA-MB-231 and the MCF7 model system. (XLSX 4123Â kb)
DOI: 10.6084/m9.figshare.c.3627530_d3
title: Additional file 4: of Molecular characterization of irinotecan (SN-38) resistant human breast cancer cell lines

description: The top 50 overexpressed genes in the SN-38 resistant MCF7 cells. (XLSX 62Â kb)
DOI: 10.6084/m9.figshare.c.3627560_d2
title: Additional file 2: Table S1. of Widespread RNA binding by chromatin-associated proteins

description: Protein antibodies. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.c.3627563_d2
title: Additional file 1: of Expression of miR-296-5p as predictive marker for radiotherapy resistance in early-stage laryngeal carcinoma

description: Table S1. Raw data of the expression level of 667 human microRNAs in LSCC samples according to the TaqMan Human MicroRNA Array assays.
DOI: 10.6084/m9.figshare.c.3627671_d2
title: Additional file 2: of Transcriptomic changes in relation to early-life events in the gilthead sea bream (Sparus aurata)

description: Blastx matches of transcripts classified in cluster 1, 2 or 3. Blastx results of transcripts in cluster 1, 2, and 3 separately. (XLSX 145Â kb)
DOI: 10.6084/m9.figshare.c.3627653_d5
title: Additional file 2: of LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects

description: Amino acid sequences from C. clementina, C. sinensis and A. thaliana kinase domains. The sequences were obtained by in-house Perl scripts using kinase coordinates from pfam database. (XLSX 108 kb)
DOI: 10.6084/m9.figshare.c.3627674_d2
title: Additional file 5: of Metabolomics of dates (Phoenix dactylifera) reveals a highly dynamic ripening process accounting for major variation in fruit composition

description: Metabolomics data from the second sample collection, measured by Metabolon (DS2). (XLSX 379 kb)
DOI: 10.6084/m9.figshare.c.3627674_d3
title: Additional file 4: of Metabolomics of dates (Phoenix dactylifera) reveals a highly dynamic ripening process accounting for major variation in fruit composition

description: Metabolomics data from the first sample collection, measured by Metabolon (DS1-bolon). (XLSX 322 kb)
DOI: 10.6084/m9.figshare.c.3627653_d7
title: Additional file 1: of LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects

description: Amino acid sequences from Arabidopsis thaliana LRR-RLKs. Dataset containing 209 LRR-RLK sequences obtained from http://arabidopsis.org/ . (XLSX 137 kb)
DOI: 10.6084/m9.figshare.c.3627698_d1
title: Additional file 11: of Transcriptomic responses of the basidiomycete yeast Sporobolomyces sp. to the mycotoxin patulin

description: Combined table of cuffdiff and BLASTx outputs for upregulated (Log2FC ≥ 2) and downregulated (Log2FC ≤ - 2) DEGs detected for Sporobolomyces sp. grown in the presence of 50 μg/ml of PAT at OD595 of ~0.25. BLASTx against existing Sporobolomyces sp. genome annotation and SGD is also shown. DEGs have been sorted from the highest Log2FC value to the smallest. In bold are indicated DEGs found also for Sporobolomyces sp. incubated in the presence of 5 μg/ml of PAT reported in Additional files 7 and 9. (XLSX 58 kb)
DOI: 10.6084/m9.figshare.c.3627653_d8
title: Additional file 6: of LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects

description: Complete list and classification of LRR-RLKs from C. clementina, C. sinensis and A. thaliana. Citrus sequences were categorized in 16 groups of LRR-RLKs. (XLSX 55 kb)