Find research datasets worth reusing

Figure 1 from: Mayorga LFSP, Vanstreels RET, Bhering RCC, Mamede N, Costa LMB, Pinheiro FCF, Reis LWD, Trazzi A, Meirelles WLC, Ribeiro AM, Siciliano S (2020) Strandings of cetaceans on the Espírito Santo coast, southeast Brazil, 1975–2015. ZooKeys 948: 129-152. https://doi.org/10.3897/zookeys.948.50468

Figure 1 Physical, biological, and human characteristics of the coast of Espírito Santo state, southeast Brazil. Legend: A, B Location of Espírito Santo and Trindade and Martim Vaz Islands C human population density, major ports, isobaths, sea surface chlorophyll-a concentration, estuaries, and bays in the study area. Data sources: (Centro Internacional de Agricultura Tropical et al. 2005, Becker et al. 2009, NASA Earth Observatory 2019).

Figure 2 from: Mayorga LFSP, Vanstreels RET, Bhering RCC, Mamede N, Costa LMB, Pinheiro FCF, Reis LWD, Trazzi A, Meirelles WLC, Ribeiro AM, Siciliano S (2020) Strandings of cetaceans on the Espírito Santo coast, southeast Brazil, 1975–2015. ZooKeys 948: 129-152. https://doi.org/10.3897/zookeys.948.50468

Figure 2 Geographic distribution of the six most frequently stranded cetacean species (excluding Megaptera novaeangliae) along the coast of Espírito Santo state, southeast Brazil, from January 1975 to September 2015. The limits of the Franciscana Management Areas (FMA) are shown in B.

Figure 5 from: Mayorga LFSP, Vanstreels RET, Bhering RCC, Mamede N, Costa LMB, Pinheiro FCF, Reis LWD, Trazzi A, Meirelles WLC, Ribeiro AM, Siciliano S (2020) Strandings of cetaceans on the Espírito Santo coast, southeast Brazil, 1975–2015. ZooKeys 948: 129-152. https://doi.org/10.3897/zookeys.948.50468

Figure 5 Annual and latitudinal distribution of recorded cetacean strandings (excluding Megaptera novaeangliae) along the coast of Espírito Santo state, southeast Brazil, from January 1975 to September 2015.

Figure 4 from: Mayorga LFSP, Vanstreels RET, Bhering RCC, Mamede N, Costa LMB, Pinheiro FCF, Reis LWD, Trazzi A, Meirelles WLC, Ribeiro AM, Siciliano S (2020) Strandings of cetaceans on the Espírito Santo coast, southeast Brazil, 1975–2015. ZooKeys 948: 129-152. https://doi.org/10.3897/zookeys.948.50468

Figure 4 Species discovery curve for the number of cetacean species occurring in Espírito Santo waters based on stranding recordings.

Gene expression counts from fibroblast, strand-specific, BCM UDN

File description: <ol> <li> Gene-level counts using the gtf file from the release 34 of GENCODE <a href="https://www.gencodegenes.org/human/release_34">https://www.gencodegenes.org/human/release_34</a> </li> <li> Split counts spanning from one exon to another using an annotation-free algorithm, therefore capturing new splice sites </li> <li> Non-split counts covering exon-intron boundaries </li> <li> Sample annotation describing each sample from the dataset </li> <li> Description file with global information from the dataset </li> </ol> Use: The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired end specifications match. Afterwards, the DROP pipeline can be used to compute expression and splicing outliers (<a href="https://github.com/gagneurlab/drop">https://github.com/gagneurlab/drop</a>). Maintainer: Vicente A. Yépez, <a href="mailto:yepez@in.tum.de">yepez@in.tum.de</a> URL: <a href="https://github.com/gagneurlab/drop/">https://github.com/gagneurlab/drop/</a>   Title: BCM UDN Fibroblast Number of samples: 139 Tissue: Fibroblast Organism: Homo sapiens Genome assembly: hg19 Gene annotation: gencode34 Disease (ICD-10: N): : D17: 1, D84: 12, E34: 2, G82: 1, H57: 3, K92: 3, M25: 18, NONE: 35, Q02: 1, Q20: 5, Q33: 2, Q89: 12, R62: 44 Strand specific: TRUE Paired end: TRUE Protocol: poly(A) enrichment Dataset contact: David Murdock, <a href="mailto:david.murdock@bcm.edu">david.murdock@bcm.edu</a> Citation: Cite both the resource using Zenodo's citation and the publication under References

Gene expression counts from blood, strand-specific, BCM UDN

File description: <ol> <li> Gene-level counts using the gtf file from the release 34 of GENCODE <a href="https://www.gencodegenes.org/human/release_34">https://www.gencodegenes.org/human/release_34</a> </li> <li> Split counts spanning from one exon to another using an annotation-free algorithm, therefore capturing new splice sites </li> <li> Non-split counts covering exon-intron boundaries </li> <li> Sample annotation describing each sample from the dataset </li> <li> Description file with global information from the dataset </li> </ol> Use: The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired end specifications match. Afterwards, the DROP pipeline can be used to compute expression and splicing outliers (<a href="https://github.com/gagneurlab/drop">https://github.com/gagneurlab/drop</a>). Maintainer: Vicente A. Yépez, <a href="mailto:yepez@in.tum.de">yepez@in.tum.de</a> URL: <a href="https://github.com/gagneurlab/drop/">https://github.com/gagneurlab/drop/</a>   Title: BCM UDN Whole Blood Number of samples: 125 Tissue: Peripheral blood Organism: Homo sapiens Genome assembly: hg19 Gene annotation: gencode34 Disease (ICD-10: N): : 1, D84: 10, E34: 2, H57: 1, K92: 4, M25: 17, NONE: 53, Q20: 3, Q33: 2, Q89: 6, R62: 26 Strand specific: TRUE Paired end: TRUE Protocol: poly(A) enrichment, no globin depletion Dataset contact: David Murdock, <a href="mailto:david.murdock@bcm.edu">david.murdock@bcm.edu</a> Citation: Cite both the resource using Zenodo's citation and the publication under References

opencc-by-4.0Nov 2020View details →

Fig. 17 in On eight species of the spider genus Synagelides Strand, 1906 from China (Araneae: Salticidae)

Fig. 17. Male palp of Synagelides spp. A, C. Holotype, retrolateral view. B, D. Male, retrolateral view. A. S. logunovi sp. nov. (TRU-Salticid-0016). B. S. forkiforma Yang, Zhu & Song, 2007 (HNU-20040428- 01). C. S. bohdanowiczi sp. nov. (TRU-Salticid-0010). D. S. palpalis Żabka, 1985 (TRU-Salticid-0053). Abbreviations: see Material and methods. Scale bars = 0.1 mm.

opennotspecifiedOct 2020View details →

FIGURES 48–51 in Huangilene, a new genus for the Miltochrista alikangiae (Strand, 1917) species-group, with descriptions of three new species from Indochina, continental China and Taiwan (Lepidoptera: Erebidae: Arctiinae: Lithosiini)

FIGURES 48–51. Huangilene spp.: male genitalia. The specimens are deposited in MWM/ZSM.

opencc-zeroDec 2017View details →

Data from: Rev7 and 53BP1/Crb2 prevent RecQ helicase-dependent hyper-resection of DNA double-strand breaks

Poly(ADP ribose) polymerase inhibitors (PARPi) target cancer cells deficient in homology-directed repair of DNA double-strand breaks (DSBs). In preclinical models, PARPi resistance is tied to altered nucleolytic processing (resection) at the 5' ends of a DSB. For example, loss of 53BP1 or Rev7/MAD2L2/FANCV derepresses resection to drive PARPi resistance, although the mechanisms are poorly understood. Long-range resection can be catalyzed by two machineries: the exonuclease Exo1, or the combination of a RecQ helicase and Dna2. Here, we develop a single cell microscopy assay that allows the distinct phases and machineries of resection to be interrogated simultaneously in living S. pombe cells. Using this assay, we find that the 53BP1 orthologue and Rev7 specifically repress long-range resection through the RecQ helicase-dependent pathway, thereby preventing hyper-resection. These results suggest that 'rewiring' of BRCA1-deficient cells to employ an Exo1-independent hyper-resection pathway is a driver of PARPi resistance.

opencc-zeroDec 2015View details →

Data from: A new plant virus discovered by immunocapture of double stranded RNA; assessment of a novel approach for viral metagenomics studies

Next-generation sequencing technologies enable the rapid identification of viral infection of diseased organisms. However, despite a consistent decrease in sequencing costs, it is difficult to justify their use in large-scale surveys without a virus sequence enrichment technique. As the majority of plant viruses have an RNA genome, a common approach is to extract the double-stranded RNA (dsRNA) replicative form, to enrich the replicating virus genetic material over the host background. The traditional dsRNA extraction is time-consuming and labour-intensive. We present an alternative method to enrich dsRNA from plant extracts using anti-dsRNA monoclonal antibodies in a pull-down assay. The extracted dsRNA can be amplified by reverse transcriptase–polymerase chain reaction and sequenced by next-generation sequencing. In our study, we have selected three distinct plant hosts: Māori potato (Solanum tuberosum), rengarenga (Arthropodium cirratum) and broadleaved dock (Rumex obtusifolius) representing a cultivated crop, a New Zealand-native ornamental plant and a weed, respectively. Of the sequence data obtained, 31–74% of the reads were of viral origin, and we identified five viruses including Potato virus Y and Potato virus S in potato; Turnip mosaic virus in rengarenga (a new host record); and in the dock sample Cherry leaf roll virus and a novel virus belonging to the genus Macluravirus. We believe that this new assay represents a significant opportunity to upscale virus ecology studies from environmental, primary industry and/or medical samples.

opencc-zeroDec 2014View details →

Data from: SNP discovery in non-model organisms: strand-bias and base-substitution errors reduce conversion rates

Single nucleotide polymorphisms (SNPs) have become the marker of choice for genetic studies in organisms of conservation, commercial or biological interest. Most SNP discovery projects in nonmodel organisms apply a strategy for identifying putative SNPs based on filtering rules that account for random sequencing errors. Here, we analyse data used to develop 4723 novel SNPs for the commercially important deep-sea fish, orange roughy (Hoplostethus atlanticus), to assess the impact of not accounting for systematic sequencing errors when filtering identified polymorphisms when discovering SNPs. We used SAMtools to identify polymorphisms in a velvet assembly of genomic DNA sequence data from seven individuals. The resulting set of polymorphisms were filtered to minimize 'bycatch'—polymorphisms caused by sequencing or assembly error. An Illumina Infinium SNP chip was used to genotype a final set of 7714 polymorphisms across 1734 individuals. Five predictors were examined for their effect on the probability of obtaining an assayable SNP: depth of coverage, number of reads that support a variant, polymorphism type (e.g. A/C), strand-bias and Illumina SNP probe design score. Our results indicate that filtering out systematic sequencing errors could substantially improve the efficiency of SNP discovery. We show that BLASTX can be used as an efficient tool to identify single-copy genomic regions in the absence of a reference genome. The results have implications for research aiming to identify assayable SNPs and build SNP genotyping assays for nonmodel organisms.

opencc-zeroDec 2014View details →

Data from: BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction

Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing inherent properties of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE) libraries and can easily extend to full transcript coverage shotgun (SHO) type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.

opencc-zeroDec 2014View details →

Data from: Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens

Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules encoded on retroelements called retrons and produced by the action of retron reverse transcriptases. Retrons are widespread in bacteria but the natural function of msDNA has remained elusive despite 30 years of study. The major roadblock to elucidation of the function of these unique molecules has been the lack of any identifiable phenotypes for mutants unable to make msDNA. We report that msDNA of the zoonotic pathogen Salmonella Typhimurium is necessary for colonization of the intestine. Similarly, we observed a defect in intestinal persistence in an enteropathogenic E. coli mutant lacking its retron reverse transcriptase. Under anaerobic conditions in the absence of msDNA, proteins of central anaerobic metabolism needed for Salmonella colonization of the intestine are dysregulated. We show that the msDNA-deficient mutant can utilize nitrate, but not other alternate electron acceptors in anaerobic conditions. Consistent with the availability of nitrate in the inflamed gut, a neutrophilic inflammatory response partially rescued the ability of a mutant lacking msDNA to colonize the intestine. These findings together indicate that the mechanistic basis of msDNA function during Salmonella colonization of the intestine is proper production of proteins needed for anaerobic metabolism. We further conclude that a natural function of msDNA is to regulate protein abundance, the first attributable function for any msDNA. Our data provide novel insight into the function of this mysterious molecule that likely represents a new class of regulatory molecules.

opennotspecifiedDec 2012View details →

FIGURES 33. Camaegeria massai n in New species and review of the Afrotropical clearwing moth genus Camaegeria Strand, 1914 (Lepidoptera: Sesiidae: Synanthedonini)

FIGURES 33. Camaegeria massai n. sp. male genitalia.

opennotspecifiedDec 2012View details →

FIGURE 32. Camaegeria auripicta Strand, 1914 in New species and review of the Afrotropical clearwing moth genus Camaegeria Strand, 1914 (Lepidoptera: Sesiidae: Synanthedonini)

FIGURE 32. Camaegeria auripicta Strand, 1914 genitalia.

opennotspecifiedDec 2012View details →

FIGURE 31. Camaegeria auripicta Strand, 1914 in New species and review of the Afrotropical clearwing moth genus Camaegeria Strand, 1914 (Lepidoptera: Sesiidae: Synanthedonini)

FIGURE 31. Camaegeria auripicta Strand, 1914 wing venation.

Figure 9 from: Sudhin PP, Caleb JTD, Sen S (2024) Additions to the knowledge on the genus Phintella Strand, 1906 (Araneae, Salticidae, Chrysillini) from India. Zoosystematics and Evolution 100(1): 31-48. https://doi.org/10.3897/zse.100.113049

Figure 9 Phintella platnicki Sudhin, Sen & Caleb, 2023, from Karnataka. A. Male, dorsal view; B. Same, ventral view; C. Same, lateral view; D. Female, dorsal view; E. Same, ventral view; F. Same, lateral view; G. Male, frontal view; H. Female, frontal view. Scale bars: 1 mm (A–H).

Figure 8 from: Sudhin PP, Caleb JTD, Sen S (2024) Additions to the knowledge on the genus Phintella Strand, 1906 (Araneae, Salticidae, Chrysillini) from India. Zoosystematics and Evolution 100(1): 31-48. https://doi.org/10.3897/zse.100.113049

Figure 8 Phintella rajbharathi sp. nov. A. Male, dorsal view; B. Same, ventral view; C. Same, lateral view; D. Same, frontal view; E. Chelicerae, ventral view; F. Left male palp, ventral view; G. Same, retrolateral view. Scale bars: 1 mm (A–C); 0.8 mm (D); 0.3 mm (E); 0.25 mm (F, G).

Figure 7 from: Sudhin PP, Caleb JTD, Sen S (2024) Additions to the knowledge on the genus Phintella Strand, 1906 (Araneae, Salticidae, Chrysillini) from India. Zoosystematics and Evolution 100(1): 31-48. https://doi.org/10.3897/zse.100.113049

Figure 7 Phintella rajbharathi sp. nov. A. Male, dorsal view; B. Same, lateral view; D, E. Same, frontal view. Photo credit A–D: Raj Bharathi.

Figure 5 from: Sudhin PP, Caleb JTD, Sen S (2024) Additions to the knowledge on the genus Phintella Strand, 1906 (Araneae, Salticidae, Chrysillini) from India. Zoosystematics and Evolution 100(1): 31-48. https://doi.org/10.3897/zse.100.113049

Figure 5 Phintella luna sp. nov. A. Female, dorsal view; B. Same, ventral view; C. Same, lateral view; D. Female epigyne, ventral view; E. Vulva, dorsal view. Scale bars: 0.5 mm (A–C); 0.2 mm (D–E).