cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3640409_d2
title: Additional file 5: Table S4. of Transcriptomes of newly-isolated Trypanosoma brucei rhodesiense reveal hundreds of mRNAs that are co-regulated with stumpy-form markers

description: Transcriptome analysis using DESeq. Sheet 1: Using only the unique gene set, transcriptomes from different isolates were compared pair-wise using DESeq. We show only the fold change and the adjusted P-values. Background colours are used only to make the pairs clear. Sheet 2: mRNAs that are most specifically increased in the LW032 and LW042 trasncriptomes relative to cBS, BT, and PC. Only genes with with adjusted P-values of less than 0.01 were considered. Of these, at least one isolate (either 42 or 32) had to show a 3-fold increase relative to cultured bloodstream forms, and the remainder of the ratios had to be at least 2× cBS or BT. B42 or 32 also had to be at least 2-fold procyclics. Comparisons with other datasets in this and subsequent sheets are indicated as follows: ST/SL Kabani; stumpy/slender ratio from [6]; ST/SL BS Jensen -stumpy/slender ratio from [7]; SLvST mRNA Capewell and ST polysomes/mRNA Capewell - data from [13]; SG/cBS: salivary gland trypanosomes relative to cultured bloodstream forms from [30]; SG/PC: salivary gland trypanosomes [30] relative to our results for cultured Lister 427 procyclic forms: cell cycle peak and amplitude: data from [31]. RITSeq: data from [28]. Sheet 3: mRNAs increased in procyclics as well as in LW032 and LW042. As for sheet 2 except that results for B42 and B32 had to be more than 0.5× the procyclic value. Sheet 4: mRNAs decreased at least two-fold in LW032 and LW042 relative to procyclics and bloodstream forms. Calculations similar to sheet 2. Sheet 5: mRNAs that were at least 3-fold higher in cBS relative to the other conditions. Sheet 6: mRNAs that were low in all parasites isolated from blood (down in BT as well as the recent isolates). (XLSX 4058 kb)
DOI: 10.15468/dl.tmuuu2
title: Occurrence Download

description: A dataset containing 3526 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Bathydraconidae"
 ]
}

 The dataset includes 3526 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033910-241126133413365/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.3640433_d3
title: Additional file 8: Table S7. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: BACS used for selected PE-4Cseq and chromatin decompaction regions. a) Location of BACs used in 3D DNA FISH experiments for the validation of df PE-4Cseq DIRs and chromatin decompaction. b) Number of CTCF, Med1, Med12, and Smc1 protein binding sites33 overlapping each BAC used for 3D DNA FISH experiments. c) Proportions of CTCF, Med1, Med12, and Smc133 protein binding sites overlapping each BAC used for 3D DNA FISH experiments normalized by BAC size. (XLSX 377 kb)
DOI: 10.6084/m9.figshare.c.3640433_d5
title: Additional file 6: Table S5. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: (a) Summary of df DIRs overlap with CTCF, Mediator, and cohesin binding sites. Column 1, Region, refers to the viewpoint assessed. Column 2, diffsites, refers to df DIRs. Column 4, no. sites and feature name corresponds to the number of DIRs that contain the specified genomic feature. Column 6, bp sites feature, presents the sum of DIRs bp which contain the specified feature. Column 8, no. features, indicates the number of features included inside DIRs. Percentages in columns 5, 7, and 9 are calculated based on the total number of regions or features in the preceding column. (b) Summary of df DIRs overlap with CTCF, Mediator, and cohesin binding sites. Column 1, Region, refers to the viewpoint assessed. Column 2, diffsites, refers to df DIRs. Column 4, no. sites and feature name corresponds to the number of DIRs that contain the specified genomic feature. Column 6, bp sites feature, presents the sum of DIRs bp which contain the specified feature. Column 8, no. features, indicates the number of features included inside the DIRs. Percentages in columns 5, 7, and 9 are calculated based on the total number of regions or features in the preceding column. (c) Summary of +  D Bl6 DIRs overlap for viewpoints 1, 2, 11, and 12 with CTCF, Mediator, and Smc1 binding sites. Column identities are as described in (a). (d) Summary of Monte Carlo simulations for assessing statistical significance of protein binding overlaps for +  D Bl6 DIRs for viewpoints 1, 2, 11, and 12. Column identities are as described in (b). Notice the significant p-values obtained for CTCF and Smc1 binding (p-val
DOI: 10.6084/m9.figshare.c.3640433_d4
title: Additional file 2: Table S1. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: (a) Positions and (b) C57Bl6/J-129S5/SvEvBrd SNP information for analyzed PE-4Cseq viewpoints on chromosome 4. Primers used for Sanger sequencing are shown. (XLSX 26Â kb)
DOI: 10.6084/m9.figshare.c.3640433_d6
title: Additional file 5: Table S4. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: Unique (a) df and (b) Df/+â   D Bl6 regions. All chromosome 4 positions are shown. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3640433_d7
title: Additional file 4: Table S3. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: Summary of median magnitude of change, direction, and number of +  D Bl6 DIRs for viewpoints 1–12. Notice how only viewpoint 5 displays an increase in contact probabilities (63 % of total regions). Viewpoints 3, 4, and 9 show a ~50 % split between regions with an increase and decrease in contact probabilities, while the rest of the viewpoints show a variable range in the decrease in interactions (60–79 % of total regions per viewpoint). (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3640433_d8
title: Additional file 3: Table S2. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: Summary of median magnitude of change, direction, and number of df DIRs for viewpoints 1, 2, 11, and 12. Notice how viewpoint 1 displays an increase in contact probabilities with surrounding sequences (64 % of total detected regions), while viewpoints 2 and 11 show mostly a decrease in interactions (60 % for viewpoint 2, and 95 % for viewpoint 11). Viewpoint 12 has both increase and decrease in interactions in approximately the same magnitude (~50 %). (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3640433_d9
title: Additional file 9: Table S8. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: Combined DE genes of three + 129 /+ Bl6 and four Df/+â   D Bl6 MEF revealed by RNA-Seq. (XLSX 170Â kb)
DOI: 10.6084/m9.figshare.c.3640433_d10
title: Additional file 13: Table S12. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: Candidate genes associated with different Monosomy 1p36 phenotypes. Their corresponding mouse homologues are shown in column 3, together with their chromosomal positions (columns 5,6). Their overlaps with df DIRs are displayed in columns 7–9, as well as the direction of change of the contact probabilities (1 = increase,–1 = decrease. Both compared to + 129 ). RNA-Seq derived expression in Df/+ Bl6 MEFs is shown in columns 11,12. Mouse gene coordinates are expressed in NCBI37/mm9 assembly, while human is GRCh38. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3640433_d12
title: Additional file 12: Table S11. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: C57Bl6/J allele-specific DE genes of three + 129 /+ Bl6 and four Df/+â   D Bl6 MEF revealed by RNA-Seq. (XLSX 48Â kb)
DOI: 10.6084/m9.figshare.c.3640433_d13
title: Additional file 11: Table S10. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: 129S5/SvEvBrd allele-specific DE genes of three + 129 /+ Bl6 and four Df/+â   D Bl6 MEF revealed by RNA-Seq. (XLSX 40Â kb)
DOI: 10.6084/m9.figshare.c.3640439_d2
title: MOESM2 of Insight into metabolic pathways of the potential biofuel producer, Paenibacillus polymyxa ICGEB2008

description: Additional file 2: List of all reactions contained in the network and the corresponding enzyme accession numbers.
DOI: 10.6084/m9.figshare.c.3640451_d2
title: Additional file 4: Table S2. of A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae

description: Upregulated mutants upregulated mutant list and ko phenotype description. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.c.3640451_d4
title: Additional file 1: Table S1. of A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae

description: Gene set: The genes identified and additional information on orthology, detection method, and expression peak. (XLSX 97Â kb)
DOI: 10.15468/dl.ksgzqw
title: Occurrence Download

description: A dataset containing 11319 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Heliomaster constantii (Delattre, 1843)"
 ]
}

 The dataset includes 11319 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033912-241126133413365/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.3640484_d1
title: Additional file 1: Table 1. of Splenic artery embolization: technically feasible but not necessarily advantageous

description: Search results and number of articles retrieved after applying the selection criteria.After the initial search, all articles were entered in a reference database (Mendeley). Table 2. Summary table of articles that met inclusion criteria after initial selection. Articles marked in grey were excluded. Table 3. Traditionally used American Association for the Surgery of Trauma (AAST) scoring system for splenic injuries. Figure 1. Algorithm for management of splenic trauma modified from Ekeh and Tugnoli.8, 32 Abbreviations: HD: hemodynamically; BP: blood pressure; FAST: Focused Assessment with Sonography for Trauma; ICU: Intensive Care Unit; SAE: splenic artery embolization; MDCT: Multidetector CT grading (TableÂ 4); NOM: non operative management; CE: contrast extravasation; IV: intravenous. (ZIP 126 kb)
DOI: 10.6084/m9.figshare.c.3640526_d1
title: Additional file 2: of Resolving Cypriniformes relationships using an anchored enrichment approach

description: Table S2. Summary of the sequence data collected and assemblies that resulted. (XLSX 91Â kb)
DOI: 10.6084/m9.figshare.c.3640559_d1
title: Additional file 2: of Towards the bridging of molecular genetics data across Xenopus species

description: Map of X. laevis, XLA9.1, 18 chromosomes on X. tropicalis , XTR9.0, 10 chromosomes. (XLSX 22301Â kb)
DOI: 10.6084/m9.figshare.c.3640559_d2
title: Additional file 3: of Towards the bridging of molecular genetics data across Xenopus species

description: Annotation of biological function of transcripts of XLA9.1 and XTR9.0. (ZIP 29029Â kb)
DOI: 10.6084/m9.figshare.c.3640562_d1
title: Additional file 2 of Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development

description: Table S2.1. List of all identified proteins. Table S2.2. Proteins with significantly changing abundance in the transition from cambium to phloem. Table S2.3. Proteins with significantly changing abundance in the transition from cambium to expansion zone. Table S2.4. Proteins with significantly changing abundance in the transition from expansion zone to xylemX1. Table S2.5. Proteins with significantly changing abundance in the transition from xylemX1 to xylemX2. Table S2.6. Proteins with significantly changing abundance in the transition from xylemX2 to xylemX3. Table S2.7. Proteins with significantly changing abundance in the transition from xylemX3 to xylemX4. Table S2.8. Subcellular localizations of proteins in the wood series analysis sorted by location designation. (XLSX 348 kb)
DOI: 10.6084/m9.figshare.c.3640562_d2
title: Additional file 1: of Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development

description: Table S1.1. Anatomical characterization and pooling scheme for tree1. Table S1.2. Anatomical characterization and pooling scheme for tree2. Table S1.3. Anatomical characterization and pooling scheme for tree3. Table S1.4. Anatomical characterization and pooling scheme for tree4. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.c.3640565_d2
title: Additional file 7: Table S7. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: Genes whose basal expression in untreated GL261(B6) tumors is either higher or lower than in untreated LLC and untreated B16F10 tumors. (XLSX 670 kb)
DOI: 10.6084/m9.figshare.c.3640565_d1
title: Additional file 9: Table S10. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: Differential gene responses to CPA in GL261(scid) and GL261(B6) tumors. (XLSX 2296 kb)
DOI: 10.6084/m9.figshare.c.3640565_d3
title: Additional file 6: Table S5. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: Negative regulators of immune response. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.c.3640565_d5
title: Additional file 1: Table S1. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: Significant gene responses induced by metronomic CPA treatment in each of the indicated tumor models. Shown in Tables S1A-S1F are genes differentially expressed between CPA-treated and control (drug-free) GL261(B6) tumors (Table S1A), LLC tumors (Table S1B), B16F10 tumors (Table S1C), and GL261(scid) tumors (Table S1D, following treatment with CPA/6d; Table S1E, treatment with CPA/9d; and Table S1F, genes common to CPA/6d and CPA/6d treatment). Treatments and other data about RNA-seq samples, including GSM accession numbers within GEO data set GSE71491, are also shown. (XLSX 3150 kb)
DOI: 10.6084/m9.figshare.c.3640565_d6
title: Additional file 3: Table S2. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: Listed are all CPA-induced upstream regulators (UPRs) as predicted by IPA for CPA-treated GL261(B6) (Table S2A), LLC (Table S2B), B16F10 (Table S2C), GL261(scid) (Table S2D; CPA/6d treatment), and GL261(scid) (Table S2E; CPA/9d treatment) tumors, respectively. (XLSX 960 kb)
DOI: 10.6084/m9.figshare.c.3640565_d7
title: Additional file 4: Table S3. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: Listing of stringent UPRs induced by CPA treatment in GL261(B6) (Table S3A), LLC (Table S3B), B16F10 (Table S3C), GL261(scid) (Table S3D; CPA/6d treatment), GL261(scid) (Table S3E; CPA/9d treatment), and GL261(scid) tumors (Table S3F; based on genes common to CPA/6d and CPA/9d treatment). (XLSX 287 kb)
DOI: 10.6084/m9.figshare.c.3640565_d8
title: Additional file 11: Table S12. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: Differential gene responses in GL261(scid) tumors induced by CPA/9d or CPA/6d treatment. (XLSX 452 kb)
DOI: 10.6084/m9.figshare.c.3640565_d9
title: Additional file 10: Table S11. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: KEGG pathways enriched in genes commonly or differentially expressed in GL261(B6) and GL261(scid) tumors in response to CPA treatment. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.c.3640565_d10
title: Additional file 13: Table S6. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: Responses to metronomic CPA in responsive tumors compared to unresponsive tumor models. Shown are the differential gene responses, and associated KEGG pathways or DAVID clusters, induced by CPA/6d treatment of GL261(B6) tumors compared to LLC and B16F10 tumors. (XLSX 718 kb)
DOI: 10.6084/m9.figshare.c.3640565_d11
title: Additional file 14: Table S9. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: Gene pathways predictive of treatment prognosis in CPA-treated tumors - We investigated whether gene pathways that may predict treatment outcome can be identified by comparing CPA-treated responsive vs. CPA-treated unresponsive tumors. (XLSX 634 kb)
DOI: 10.6084/m9.figshare.c.3640565_d12
title: Additional file 12: Table S13. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: KEGG pathways and DAVID clusters that are associated with genes preferentially up regulated (&gt;1.33-fold) in GL261(scid) tumors treated with CPA/6d (Table S13A, B) or CPA/9d (Table S13C, D). Also shown (Table S13E) are KEGG pathways enriched in the set of genes expressed at a level 1.5-fold higher level in GL261(scid) tumors treated on the CPA/9d schedule than those treated on CPA/6d schedule. (XLSX 55 kb)
DOI: 10.6084/m9.figshare.c.3640565_d13
title: Additional file 5: Table S4. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: KEGG pathways enriched in genes up regulated or down regulated by CPA treatment in GL261(B6) tumors (Table S4A), LLC tumors (Table S4B), and B16F10 tumors (Table S4C). (XLSX 32 kb)
DOI: 10.6084/m9.figshare.c.3640565_d14
title: Additional file 8: Table S8A-F. of Metronomic cyclophosphamide activation of anti-tumor immunity: tumor model, mouse host, and drug schedule dependence of gene responses and their upstream regulators

description: KEGG pathways and DAVID clusters enriched in genes that are specifically expressed at a higher or a lower level in untreated GL261(B6) tumors when compared to LLC and B16F10 tumors and in the sets of genes that respond to CPA/6d treatment. (XLSX 186 kb)
DOI: 10.6084/m9.figshare.c.3640595_d4
title: Additional file 4: Table S4. of Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): implications for medical, veterinary and forensic research

description: A list showing the distribution of glutathione S-transferases in the male and female P. regina genomes. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3640595_d5
title: Additional file 2: Table S2. of Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): implications for medical, veterinary and forensic research

description: BLASTn (27 hits) and BLASTp (115 hits) results for antimicrobial peptide queries using D. melanogasterâ  s homologous gene and protein sequences as queries. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.c.3640595_d7
title: Additional file 5: Table S5. of Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): implications for medical, veterinary and forensic research

description: A list of metabolic enzymes that belong to the esterases and hydrolases family that are predicted to be linked with insecticide resistance. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.c.3640595_d13
title: Additional file 1: Table S1. of Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): implications for medical, veterinary and forensic research

description: tBLASTx results of contigs with D. melanogasterâ  s homologus gene sequences of gustatory receptors, odorant binding proteins, odorant receptors and ionotropic receptors. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.c.3640595_d16
title: Additional file 11: Table S9. of Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): implications for medical, veterinary and forensic research

description: List of biological KEGG pathways extracted from the annotations of the male and female predicted protein-encoding genes. Each tab represents biological KEGG pathways extracted from the male and female genomes. (XLSX 66Â kb)
DOI: 10.6084/m9.figshare.c.3640595_d22
title: Additional file 3: Table S3. of Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): implications for medical, veterinary and forensic research

description: A list showing the distribution of cytochrome P450 monooxygenases families in the male and female P. regina genomes. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.c.3640604_d3
title: Additional file 9: Table S2. of Identification of the genes involved in odorant reception and detection in the palm weevil Rhynchophorus ferrugineus, an important quarantine pest, by antennal transcriptome analysis

description: Percent identity of insect SNMPs. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3640640_d1
title: Additional file 2: of Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations

description: The EC2KEGG output for the RV1423 analysis sorted in ascending order by the FDR value. (XLSX 58Â kb)
DOI: 10.6084/m9.figshare.c.3640640_d2
title: Additional file 1: of Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations

description: Summary data for PSAT analysis of RV1423. (XLSX 1543Â kb)
DOI: 10.6084/m9.figshare.c.3640643_d4
title: Additional file 8: Tabular data 2. of Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice

description: List of drought responsive miRNAs and their putative target genes and their expression patterns of both under drought conditions. (XLSX 101 kb)
DOI: 10.6084/m9.figshare.c.3640643_d3
title: Additional file 6: Table S3. of Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice

description: List of miRNAs that are constitutive pattern of high expression and low expression level. 1 Bold in miRNAs ID, rice specific drought responsive miRNAs; 2 RPKM, Reads Per Kilobase of transcript per Million mapped reads; 3 C, control; 4 1d, drought treatment for 1 day; 5 2d, drought treatment for 2 days; 6 3d, drought treatment for 3 days; 7 log2 ratio, log2(drought treatment / control), 8 Red, up-regulation by drought; Blue, down-regulation by drought Abbreviations: At, Arabidopsis thaliana; Bd, Brachypodium distachyon; Gm, Glycine max; Hv, Hordeum vulgare; Mt, Medicago truncatula; Me, Manihot esculenta; Pv, Phaseolus vulgaris; Peu, Populus euphratica; Ptc, Populus trichocarpa; Ppe, Prunus persica; Pte: Populus tremula; Pto, Populus tomentosa; Td, Triticum dicoccoides; Tt, Triticum turgidum; Os, Oryza sativa; Vu, Vigna unguiculata; Zm, Zea mays [10, 15]. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.c.3640643_d5
title: Additional file 1: Table S1. of Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice

description: Information about the RNA-seq data obtained by Illumina Hi-seq 2500 sequencing. (XLSX 12 kb)