cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3643421_d13
title: Additional file 2: Table S1. of Recombination-driven generation of the largest pathogen repository of antigen variants in the protozoan Trypanosoma cruzi

description: Newly Annotated and Modified TcTS. (a) 735 TcTS genes annotated as “real”; full-length containing both signal peptide and GPI anchor motifs and whose amino acid translations resulted in no in-frame stop codons; (b) List of all TcTS genes; (c) List of newly annotated TcTS and those whose bounds were modified in this study. Temporary IDs were assigned to each sequence by adding “2000” followed by a unique identifier for each newly discovered sequence on a particular contig and by pre-pending “1000” to the unique identifier for each modified sequence. (d) Locations of all TcTS genes and (e) newly identified, and modified TcTS on the T. cruzi chromosomes. Nucleotide sequences are indicated as “full-length” if they encoded both a signal sequence and GPI-anchor addition site, “partial” if encoding a signal sequence but not a GPI anchor addition site, and “pseudogene” if lacking a signal sequence. Sequences whose translations contain in-frame stop codon(s) are annotated with “in-frame stop” (f) List of 40 “model” full-length TcTS genes of at least 2Kb in length and containing both a signal peptide and GPI anchor motif. (XLSX 572 kb)
DOI: 10.15468/dl.cpkpy7
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Anopheles hancocki Edwards, 1929"
 ]
}

 The dataset includes 49 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033997-241126133413365/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.3643433_d7
title: Additional file 12: Table S1. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

description: (XLSX 81Â kb)
DOI: 10.6084/m9.figshare.c.3643481_d4
title: MOESM4 of Compression distance can discriminate animals by genetic profile, build relationship matrices and estimate breeding values

description: Additional file 4: Table S1. Genome regions with extreme differences in CEh between BB and TC cattle. This file identifies the genomic regions that are different between BB and TC cattle as determined by sliding window CEh.
DOI: 10.6084/m9.figshare.c.3643493_d4
title: Additional file 10: Tables S5A and S5B. of Distinct gene expression program dynamics during erythropoiesis from human induced pluripotent stem cells compared with adult and cord blood progenitors

description: Both relate to Fig.Â 4 and contain annotations, linear expression values, statistical parameters and fold changes of differentially expressed genes between different populations during maturation of Adult and hiPSC Erythroblasts in SEM-i. Inclusion criteria for differentially expressed genes: B value of at least 2.945, p-value below 0.01, fold change of at least 2, and expression levels in all replicates at any population of at least 100. Erythroblasts were cultured for between 0 and 14 days (d0-d14). Upregulated and downregulated genes are listed separately in Table S5B. (XLSX 5326 kb)
DOI: 10.6084/m9.figshare.c.3643493_d10
title: Additional file 20: Table S4. of Distinct gene expression program dynamics during erythropoiesis from human induced pluripotent stem cells compared with adult and cord blood progenitors

description: Relates to Fig.Â 3. Annotations, linear expression values, statistical parameters and fold changes of genes DE (B value at least 2.945, p-value below 0.01, fold change at least 2, and expression levels in all replicates at any population at least 100) between different populations during maturation of Adult Erythroblasts (AB-erythroblasts) in SEM-F or SEM-i, cultured for between 0 and 14 days (d0-d14). (XLSX 10526 kb)
DOI: 10.6084/m9.figshare.c.3643493_d14
title: Additional file 2: of Distinct gene expression program dynamics during erythropoiesis from human induced pluripotent stem cells compared with adult and cord blood progenitors

description: Tables S1A and S1B. Both relate to Fig.Â 1. (XLSX 9540 kb)
DOI: 10.15468/dl.9twmnb
title: Occurrence Download

description: A dataset containing 265 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Anopheles hyrcanus (Pallas, 1771)"
 ]
}

 The dataset includes 265 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033998-241126133413365/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.3643523_d1
title: MOESM1 of Malaria vector populations across ecological zones in Guinea Conakry and Mali, West Africa

description: Additional file 1. Molecular attribute data for mosquitoes collected across ecological zones in Guinea and Mali.
DOI: 10.6084/m9.figshare.c.3643526_d3
title: MOESM1 of Functional demonstrations of starch binding domains present in Ostreococcus tauri starch synthases isoforms

description: Additional file 1: Table S1. Sequences Retrieved from Similarity Searches.
DOI: 10.6084/m9.figshare.c.3643532_d1
title: Additional file 1: Table S1. of Deciphering mechanisms of drug sensitivity and resistance to Selective Inhibitor of Nuclear Export (SINE) compounds

description: MetaCore analysis of fold changes in expression of all genes in SINE compound-resistant versus parental cells post-treatment. FDR = Benjamini-Hochberg False Discovery Rate. Red = positive, blue = negative, color intensity corresponds to fold change magnitude. Table S2. MetaCore analysis of fold changes in expression of genes with p53 regulatory elements in SINE compound-resistant versus parental cells post-treatment. FDR = Benjamini-Hochberg False Discovery Rate. In the p53 regulation column, “+”, “-“and “?” correspond to positive, negative, and uncertain regulation by p53, respectively. Red = positive, blue = negative, color intensity corresponds to fold change magnitude. (XLSX 104 kb)
DOI: 10.6084/m9.figshare.c.3643535_d1
title: Additional file 1: Table S1. of Finding an appropriate equation to measure similarity between binary vectors: case studies on Indonesian and Japanese herbal medicines

description: The mean of AUCs between equations and disease classes in Jamu data. (XLSX 50Â kb)
DOI: 10.6084/m9.figshare.c.3643550_d2
title: Additional file 9: Table S6. of Mapping the sex determination locus in the hÄ puku (Polyprion oxygeneios) using ddRAD sequencing

description: Primer and sequence information for allele-specific SNP assays. (CSV 597 bytes)
DOI: 10.6084/m9.figshare.c.3643550_d3
title: Additional file 2: Table S1. of Mapping the sex determination locus in the hÄ puku (Polyprion oxygeneios) using ddRAD sequencing

description: Detailed information for each sample used. Sample ID, Barcodes, Read recovered etc. (CSV 12Â kb)
DOI: 10.6084/m9.figshare.c.3643550_d4
title: Additional file 6: Table S4. of Mapping the sex determination locus in the hÄ puku (Polyprion oxygeneios) using ddRAD sequencing

description: Female only genetic map (positions and RAD locus sequences). (CSV 122Â kb)
DOI: 10.6084/m9.figshare.c.3643550_d6
title: Additional file 11: Table S7. of Mapping the sex determination locus in the hÄ puku (Polyprion oxygeneios) using ddRAD sequencing

description: Synteny comparisons. Location of each marker retrieved in tested genomes. For each marker, the chromosome ID, start and end location of the best BLASTn hit is reported. (CSV 138Â kb)
DOI: 10.6084/m9.figshare.c.3643550_d8
title: Additional file 3: Table S2. of Mapping the sex determination locus in the hÄ puku (Polyprion oxygeneios) using ddRAD sequencing

description: Full genotypes for mapping family. (CSV 301Â kb)
DOI: 10.6084/m9.figshare.c.3643583_d5
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_d6
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_d7
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: 10.15468/dl.xvygzg
title: Occurrence Download

description: A dataset containing 183 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Anopheles labranchiae Falleroni, 1926"
 ]
}

 The dataset includes 183 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033999-241126133413365/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_d12
title: Additional file 8: Table S4. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

description: Comparison of the off-target prediction sensitivity of the CRISPR Design website ( http://crispr.mit.edu/ ), CRISPOR, and CasOffFinder by the number of mismatches. Only off-targets with the PAM NGG were taken into account as the non-standard PAMs differ among the tools. Shown are the number of mismatches in the first columns, then over three columns the number of off-targets predicted for each tool, then two columns with the number of sites found by CRISPOR and CasOffFinder but not by the MIT site, then two columns with the number of sites found by the MIT site but not the other two tools (always 0). The next column shows an example sequence that was missed by the MIT site. The final column contains the distribution of mismatches for each nucleotide over the length of the guide sequence, for all sequences missed by the MIT site. (XLS 30 kb)
DOI: 10.6084/m9.figshare.c.3643583_d13
title: Additional file 1: Table S1. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

description: Detailed information about CRISPR/Cas9 off-target studies, including first author, PMID, name of the primary assay, type of genome change detected, cell type, sensitivity, number of guides studied, off-targets found, and whether the off-targets found with the primary assay where subsequently validated by PCR and sequencing. (XLS 36 kb)
DOI: 10.6084/m9.figshare.c.3643583_d14
title: Additional file 4: Table S2. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

description: Reproducibility of the guide EMX1 GAGTCCGAGCAGAAGAAGAAGGG across three different assays. Shown are the numbers and locations of the mismatches, the off-target score, modification frequencies found by the different studies, and whether the off-target was predicted by the CRISPR Design website ( http://crispr.mit.edu/ ). (XLS 31 kb)
DOI: 10.6084/m9.figshare.c.3643583_d16
title: Additional file 15: Table S7. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

description: Details of the Teboul mouse dataset of this study. (XLS 70 kb)
DOI: 10.6084/m9.figshare.c.3643583_d17
title: Additional file 11: Table S6. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

description: Correlations between knock-out efficiency results in different studies and cell types. (XLS 40 kb)
DOI: 10.6084/m9.figshare.c.3643589_d3
title: Additional file 2: Table S1. of Evaluation of folate receptor 1 (FOLR1) mRNA expression, its specific promoter methylation and global DNA hypomethylation in type I and type II ovarian cancers

description: Multivariate survival analysis for FOLR1 expression in the entire cohort. Cut-off for FOLR1 expression = Median value in cancers. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3643643_d1
title: Additional file 4: of 
                     De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis

description: L. williamsii unigenes. (ZIP 7124 kb)
DOI: 10.6084/m9.figshare.c.3643643_d2
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.c.3643643_d3
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_d4
title: Additional file 5: Alignment of Pyridoxal DeC protein domain.  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.c.3643643_d5
title: Additional file 1: TrnL-trnF intergenic spacer. of 
                     De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis

description: (FASTA 978 bytes)
DOI: 10.6084/m9.figshare.c.3643643_d6
title: Additional file 3: Table S1. of 
                     De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis

description: Alkaloids found in the ethanol extracts of buttons and roots of L. williamsii. Table S2. Reads statistics of the L. williamsii dataset. Table S3. Annotation of Lophophora williamsii unigenes. (TAIRv10; http://www.arabidopsis.org/ and NCBI; ftp://ftp.ncbi.nih.gov/refseq/release/plant/ Table S4. Funtional classification of L williamsii unigenes based on Arabidopsis GO annotation. Table S5. Detailed information for L. williamsii unigenes mapped on KEGG pathways. Table S6. Expression profile matrix of L. williamsii unigenes. Table S7. Preferentially expressed unigenes in specific organs (buttons and roots) of L. williamsii. (XLSX 16694 kb)
DOI: 10.6084/m9.figshare.c.3643643_d7
title: Additional file 6: Alignment of PPO1-KFDV protein domain. of 
                     De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis

description: (FASTA 1009 bytes)
DOI: 10.6084/m9.figshare.c.3643643_d8
title: Additional file 7: Alignment of αKG-dependent dioxigenase proteins. of 
                     De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis

description: (FASTA 33 kb)
DOI: 10.6084/m9.figshare.c.3643649_d1
title: Additional file 4: of Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia

description: The protein complexes involved in SDMGs and SCZCGs. (XLSX 27Â kb)
DOI: 10.6084/m9.figshare.c.3643649_d4
title: Additional file 1: of Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia

description: Differentially methylated genes with differential expression databases. (XLSX 170Â kb)
DOI: 10.15468/dl.vshpr3
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Anopheles litoralis King, 1932"
 ]
}

 The dataset includes 9 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034000-241126133413365/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.3643649_d2
title: Additional file 2: of Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia

description: Pathway enrichment analysis of SDMGs, hypermethylating SDMGs and SDMGs with level 1 PPI. (XLSX 576Â kb)
DOI: 10.6084/m9.figshare.c.3643649_d3
title: Additional file 3: of Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia

description: The shared common genes of 688 SDMG promoters and PsyGeNET. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.c.3643700_d1
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: 10.6084/m9.figshare.c.3643706_d1
title: Additional file 1: Table S1. of Paratransgenesis to control malaria vectors: a semi-field pilot study

description: Bacterial composition (number of reads) at phylum, class, order, family, genus level for sugar -fed and antibiotic-treated An. gambiae mosquitoes. (XLS 106 kb)
DOI: 10.6084/m9.figshare.c.3643712_d1
title: Additional file 1: of An investigation to assess ankle mobility in healthy individuals from the application of multi-component compression bandages and compression hosiery

description: Raw data from gait investigation. (XLSX 256Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d4
title: Additional file 18: Table S10. 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 NZ combination. (XLSX 45Â kb) (XLSX 41Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d5
title: Additional file 16: Table S8. 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 NZ combination. (XLSX 53Â kb) (XLSX 49Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d6
title: Additional file 14: Table S6. 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 changed-tissues and global jiDE genes of the NM combination. (XLSX 16Â kb) (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3643808_d3
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)
DOI: 10.6084/m9.figshare.c.3643814_d2
title: Additional file 3: Table S2. of Codon bias and the folding dynamics of the cystic fibrosis transmembrane conductance regulator

description: SNPs effects on CFTR mRNA secondary structure. The SNPs with significant p - values (&lt;0.2) are marked grey. Furthermore, sSNPs with p - value p
DOI: 10.6084/m9.figshare.c.3643814_d4
title: Additional file 6: Table S3. of Codon bias and the folding dynamics of the cystic fibrosis transmembrane conductance regulator

description: CADD analysis of CFTR SNPs. SNPs that may affect splicing are marked bold. SNPs with C-score significantly higher than whole genome median are marked light grey, while SNPs with highest quartile C-scores are marked dark grey. (XLSX 28Â kb)