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Making Data Work: A Systematic Mapping of Collaborative Data Curation Practices

This file contains dataset associated with the paper Making Data Work: A Systematic Mapping of Collaborative Data Curation Practices

opencc-by-4.0Apr 2022View details →

Systematic analysis of alternative splicing in time course data using Spycone

Spycone is available as a python package that provides systematic analysis of time course transcriptomics data. Figure 1 shows the workflow of Spycone. It uses gene or isoform expression and a biological network as an input. It employs the sum of changes of all isoforms relative abundance (total isoform usage) across time points to detect IS events. It further provides downstream analysis such as clustering by total isoform usage, gene set enrichment analysis, network enrichment, and splicing factors analysis. The SARS-Cov-2 infection and cancer dataset are used as an application demonstration for our Spycone tool and a simulation dataset is used for benchmark analysis.  The rhinovirus dataset and SARS-Cov-2 infection (3 time points) for the tutorial in the documentation are included here.  The simulated dataset from the 2 models described in the manuscript are uploaded as zen_simdata_{model}_{noise}.csv. A gtf file used in the splicing factor analysis, both in the manuscript and tutorial. Derived from ensembl GRCh38.99.

Fig. 3 in Systematic evaluation of cryptic freshwater snails from central Chile, including the enigmatic Littoridina santiagensis (Gastropoda, Truncatelloidea)

Fig. 3. Potamolithus santiagensis (Biese, 1944) comb. nov., Yeso Spring, Chile. A. Shell imaged using SEM. B–D. Shell of the same specimen photographed under a stereo microscope (frontal, dorsal, lateral views). E. Protoconch. F–G. Opercula of two specimens (outer, inner sides, respectively). H. Head of a female. I. Head of another female having a nuchal node. J. Anterior-central section of radular ribbon. K. Central teeth. Abbreviations: f = foot; h = head; l = lip; lt = left tentacle; nn = nuchal node; rt = right tentacle. Scale bars: A–D = 1.0 mm; E = 250 μm; F–G = 500 μm; H–I = 0.5 mm; J = 50 μm; K = 10 μm.

Fig. 2 in Systematic evaluation of cryptic freshwater snails from central Chile, including the enigmatic Littoridina santiagensis (Gastropoda, Truncatelloidea)

Fig. 2. Shells of truncatelloidean freshwater snails observed in the present study. A–B. Slender morphotype from El Yeso Spring (A) and Lo Carreño (B) assigned to Potamopyrgus antipodarum (Gray, 1843). C–E. Thicker morphotype from El Yeso Spring (C), Lo Carreño (D) and El Colorado (E) assigned to Potamolithus santiagensis (Biese, 1944) comb. nov. F. Thicker morphotype from Viña Casas del Maule assigned to Potamolithus sp. Scale bar = 1 mm.

Fig. 1 in Systematic evaluation of cryptic freshwater snails from central Chile, including the enigmatic Littoridina santiagensis (Gastropoda, Truncatelloidea)

Fig. 1. "Littoridina" santiagensis Biese, 1944. A. The only drawings of a specimen of the species taken from the original description by Biese (1944). B. Lectotype housed at the Museo Nacional de Historia Natural, Santiago, Chile (MNHNCL) (after Collado et al. 2011).

Fig. 5 in Systematic evaluation of cryptic freshwater snails from central Chile, including the enigmatic Littoridina santiagensis (Gastropoda, Truncatelloidea)

Fig. 5. Bayesian tree based on COI sequences. Numbers at nodes indicate posterior probability values (only given if Ż 0.95). Names in bold refer to new sequences reported in this paper. Numbers following taxa refer to GenBank sequences.

Fig. 6 in Documenting tenebrionid diversity: progress on Blaps Fabricius (Coleoptera, Tenebrionidae, Tenebrioninae, Blaptini) systematics, with the description of Fve new species

Fig. 6. Bayesian maximum consensus tree resulting from the analysis of the combined molecular and morphological dataset carried out with MrBayes. Support of nodes is indicated using empty circles (for PP> 0.50) and flled circles for PP> 0.95). Species groups for Blaps belonging to section I are highlighted using transparent coloured frames. Paraphyletic species groups are highlighted using bracketed names; orange arrows are also used to highlight the placement of the fve new species. For illustrative purposes, the habitus of some adults are fgured on the right side of the fgure; on the left upper side, the habitus of the fve new species are also presented (all photographs were taken by L. Soldati).

Fig. 3 in Documenting tenebrionid diversity: progress on Blaps Fabricius (Coleoptera, Tenebrionidae, Tenebrioninae, Blaptini) systematics, with the description of Fve new species

Fig. 3. Blaps maldesi Soldati sp. nov. A. ♂, habitus (dorsal view). B. ♂, habitus (lateral view). C. ♂, habitus (ventral view). D. ♂, left antenna (dorsal view). E. ♂, mucro (dorsal view). F. ♂, mucro (lateral view). G. ♀, mucro (dorsal view). H. ♂, aedeagus (ventral view). I. ♂, aedeagus (lateral view). Scale bars: A–C = 10 mm; D = 5 mm; E–G = 2 mm; H–I = 1 mm.

Fig. 1 in Documenting tenebrionid diversity: progress on Blaps Fabricius (Coleoptera, Tenebrionidae, Tenebrioninae, Blaptini) systematics, with the description of Fve new species

Fig. 1. Blaps effeminata Soldati sp. nov. A. ♂, habitus (dorsal view). B. ♂, habitus (lateral view). C. ♂, habitus (ventral view). D. ♂, left antenna (dorsal view). E. ♂, mucro (dorsal view). F. ♂, mucro (lateral view). G. ♀, mucro (dorsal view). H. ♂, aedeagus (ventral view). I. ♂, aedeagus (lateral view). Scale bars: A–C = 10 mm; D = 5 mm; E–G = 2 mm; H–I = 3 mm.

Fig. 5 in Documenting tenebrionid diversity: progress on Blaps Fabricius (Coleoptera, Tenebrionidae, Tenebrioninae, Blaptini) systematics, with the description of Fve new species

Fig. 5. Blaps teocchii Soldati sp. nov. A. ♂, habitus (dorsal view). B. ♂, habitus (lateral view). C. ♂, habitus (ventral view). D. ♂, left antenna (dorsal view). E. ♂, mucro (dorsal view). F. ♂, mucro (lateral view). G. ♀, mucro (dorsal view). H. ♂, aedeagus (ventral view). I. ♂, aedeagus (lateral view). Scale bars: A–C = 10 mm; D = 5 mm; E–G = 2 mm; H–I = 1.5 mm.

Fig. 2 in Documenting tenebrionid diversity: progress on Blaps Fabricius (Coleoptera, Tenebrionidae, Tenebrioninae, Blaptini) systematics, with the description of Fve new species

Fig. 2. Blaps intermedia Soldati sp. nov. A. ♂, habitus (dorsal view). B. ♂, habitus (lateral view). C. ♂, habitus (ventral view). D. ♂, left antenna (dorsal view). E. ♂, mucro (dorsal view). F. ♂, mucro (lateral view). G. ♀, mucro (dorsal view). H. ♂, aedeagus (ventral view). I. ♂. aedeagus (lateral view). Scale bars: A–C = 10 mm; D = 5 mm; E–I = 2 mm.

Fig. 10 in Phylogenetic analysis and systematics of the Acrapex unicolora Hampson species complex (Lepidoptera, Noctuidae, Noctuinae, Apameini), with the description of Fve new species from the Afrotropics

Fig. 10. Maximum likelihood tree resulting from the analysis of the combined dataset carried out with IQ-TREE. Support of major nodes is displayed as BV (only BV> 50% are shown). On the right, corresponding adult habitus (for species belonging to the A. unicolora species group) are also included for illustrative purposes. Results of PTP analyses are fgured using coloured branches and vertical side bars. Putative molecular species clusters are indicated using transitions between blue-coloured branches to red-coloured branches (vertical bars are also informative).

Fig. 8 in Phylogenetic analysis and systematics of the Acrapex unicolora Hampson species complex (Lepidoptera, Noctuidae, Noctuinae, Apameini), with the description of Fve new species from the Afrotropics

Fig. 8. Adults of species of Acrapex. – A–D. A. parvaclara Berio, 1973. A. ♂, upper side. B. ♂, under side. C. ♀, upper side. D. ♀, under side. – E–F. A. simillima le Ru sp. nov. E. ♀, upper side. F. ♀, under side. – G–J. A. unicolora (Hampson, 1910). G. ♂, upper side. H. ♂, under side. I. ♀, upper side. J. ♀, under side. Scale bars = 10 mm.

Fig. 9. Last instar larva. A in Phylogenetic analysis and systematics of the Acrapex unicolora Hampson species complex (Lepidoptera, Noctuidae, Noctuinae, Apameini), with the description of Fve new species from the Afrotropics

Fig. 9. Last instar larva. A. Acrapex simillima le Ru sp. nov. B. A. unicolora (Hampson, 1910). Scale bar = 10 mm.

Fig. 7 in Phylogenetic analysis and systematics of the Acrapex unicolora Hampson species complex (Lepidoptera, Noctuidae, Noctuinae, Apameini), with the description of Fve new species from the Afrotropics

Fig. 7. Adults of species of Acrapex. – A–E. A. mediopuncta (Bowden, 1956). A. ♂, upper side. B. ♂, under side. C. ♀, upper side. D. ♀, under side. E. ♀, original labels from BMNH. – F–G. A. miscantha le Ru sp. nov. F. ♀, upper side. G. ♀, under side. Scale bars = 10 mm.

Fig. 6 in Phylogenetic analysis and systematics of the Acrapex unicolora Hampson species complex (Lepidoptera, Noctuidae, Noctuinae, Apameini), with the description of Fve new species from the Afrotropics

Fig. 6. Adults of species of Acrapex. – A–B. A. kavumba le Ru sp. nov. A. ♂, upper side. B. ♂, under side. – C–F. A. kiakouama le Ru sp. nov. C. ♂, upper side. D. ♂, under side. E. ♀, upper side. F. ♀, under side. – G–I. A. malagasy Viette, 1967. G. ♂, upper side. H. ♂, under side. I. ♂, original labels from MNHH. Scale bars = 10 mm.

Fig. 3 in Phylogenetic analysis and systematics of the Acrapex unicolora Hampson species complex (Lepidoptera, Noctuidae, Noctuinae, Apameini), with the description of Fve new species from the Afrotropics

Fig. 3. Female genitalia of species of Acrapex. A. A. cuprescens (Hampson, 1910). B. A. kafula le Ru sp. nov. C. A. kiakouama le Ru sp. nov. D. A. mediopuncta (Bowden, 1956). E. A. miscantha le Ru sp. nov. F. A. parvaclara Berio, 1973. G. A. simillima le Ru sp. nov. H. A. unicolora (Hampson, 1910). Scale bars = 1 mm.

Fig. 4 in Documenting tenebrionid diversity: progress on Blaps Fabricius (Coleoptera, Tenebrionidae, Tenebrioninae, Blaptini) systematics, with the description of Fve new species

Fig. 4. Blaps nitiduloides Soldati sp. nov. A. ♂, habitus (dorsal view). B. ♂, habitus (lateral view). C. ♂, habitus (ventral view). D. ♂, left antenna (dorsal view). E. ♂, mucro (dorsal view). F. ♂, mucro (lateral view). G. ♀, mucro (dorsal view). H. ♂, aedeagus (ventral view). I. ♂, aedeagus (lateral view). Scale bars: A–C = 10 mm; D = 5 mm; E–I = 2 mm.

Fig. 1 in Phylogenetic analysis and systematics of the Acrapex unicolora Hampson species complex (Lepidoptera, Noctuidae, Noctuinae, Apameini), with the description of Fve new species from the Afrotropics

Fig. 1. Adults of species of Acrapex. – A–F. A. cuprescens (Hampson, 1910). A. ♂, upper side. B. ♂, under side. C. ♂, original labels from BMNH. D. ♀, original labels from BMNH. E. Upper side. F. Under side. – G–J. A. kafula le Ru sp. nov. G. ♂, upper side. H. ♂, under side. I. ♀, upper side. J. ♀, under side. Scale bars = 3 mm.

Fig. 2 in Phylogenetic analysis and systematics of the Acrapex unicolora Hampson species complex (Lepidoptera, Noctuidae, Noctuinae, Apameini), with the description of Fve new species from the Afrotropics

Fig. 2. Male genitalia of species of Acrapex. – A, I. A. cuprescens (Hampson, 1910). – B, J. A. kafula le Ru sp. nov. – C, K. A. kavumba le Ru sp. nov. – D, L. A. kiakouama le Ru sp. nov. – E, M. A. malagasy Viette, 1967. – F, N. A. mediopuncta (Bowden, 1956). – G, O. A. parvaclara Berio, 1973. – H, P. A. unicolora (Hampson, 1910). Scale bars = 0.5 mm.