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Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens
<p>This repo contains Seurat objects, differential expression analysis results, and pathway gene lists for the manuscript "Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens"<br>List of files:</p> <p>1. Seurat_object_IFNB_Perturb_seq.rds: Seurat object of the Perturb-seq data for Interferon-beta pathway<br>2. Seurat_object_IFNG_Perturb_seq.rds: Seurat object of the Perturb-seq data for Interferon-gamma pathway<br>3. Seurat_object_TNFA_Perturb_seq.rds: Seurat object of the Perturb-seq data for TNF-alpha pathway<br>4. Seurat_object_TGFB1_Perturb_seq.rds: Seurat object of the Perturb-seq data for TGF-beta1 pathway<br>5. Seurat_object_INS_Perturb_seq.rds: Seurat object of the Perturb-seq data for insulin pathway<br>6. Pathway_genelist.rds: The pathway gene lists from MultiCCA analysis<br>7. Pathway_Exclusive_genelist.rds: The pathway exclusive gene lists generated from Pathway_genelist.rds<br>8. HClust_Pathway_celltype_specific_genelist.rds: The cell-line specific pathway gene lists from hierarchical clustering analysis independently done on each cell line<br>9. DE_results_all_pathway.zip: The DE test results for all the regulators, cell lines, and pathways (from Mixscale weighted DE test.)<br>10. Bulk_RNAseq_Seurat_object_IFNG_and_TGFB_stim.rds: Seurat object for the bulk RNA-seq data for interferon-gamma and TGF-beta stimulation experiments<br>11. Parse_Guide_Capture_Protocol.pdf: The guide RNA capture protocol developed for Parse Evercode Whole Transcriptome kit</p>
Fig. 3. Karyotypes after FISH with 5S in Contributions to the systematic of Pimelodidae (Osteichthyes, Siluriformes): basic and molecular cytogenetics on seven species of Pimelodus from three Brazilian hydrographic systems
Fig. 3. Karyotypes after FISH with 5S rDNA probes (red) and 18S rDNA probe (green). a. Pimelodus absconditus; b. Pimelodus britskii; c. Pimelodus maculatus; d. Pimelodus microstoma; e. Pimelodus mysteriosus; f. Pimelodus ortmanni; g. Pimelodus paranaensis. Scales bar = 10 μm.
Fig. 2. Karyotypes arranged from C-banded chromosomes. a in Contributions to the systematic of Pimelodidae (Osteichthyes, Siluriformes): basic and molecular cytogenetics on seven species of Pimelodus from three Brazilian hydrographic systems
Fig. 2. Karyotypes arranged from C-banded chromosomes. a. Pimelodus absconditus; b. Pimelodus britskii; c. Pimelodus maculatus; d. Pimelodus microstoma; e. Pimelodus mysteriosus; f. Pimelodus ortmanni; g. Pimelodus paranaensis. B chromosomes in the boxes. Scales bar = 10 μm.
Fig. 5 in Contributions to the systematic of Pimelodidae (Osteichthyes, Siluriformes): basic and molecular cytogenetics on seven species of Pimelodus from three Brazilian hydrographic systems
Fig. 5. Cytogenetics data and phylogenetic relationships between Pimelodidae (modified from Lundberg et al., 2011). N= Neopimelodines; S= Sorubimines; CP= Calophysus-Pimelodus Clade; C = Calophysines; PI = Pimelodus Group; 2n = number diploid; p = short arm; q = long arm; S = simple; M = multiple.
Fig. 5 in Molecular systematics and biogeography of the Hemigalinae civets (Mammalia, Carnivora)
Fig. 5. Median-joining haplotype network for Chrotogale owstoni Thomas, 1912 Cytb haplotypes (top: 837 bp, bottom: 235 bp). The size of each circle is proportional to the haplotype frequency. White = central Vietnam clade; grey = northern Vietnam clade, black = China.
Fig. 4 in Molecular systematics and biogeography of the Hemigalinae civets (Mammalia, Carnivora)
Fig. 4. Median-joining haplotype network for Hemigalus derbyanus (Gray, 1837) Cytb haplotypes (top: 837 bp, bottom: 253bp). The size of each circle is proportional to the haplotype frequency. The colours of the haplotypes correspond to those on the map: black = Borneo; dark grey = Siberut Island (Mentawai Islands); light grey = Penang Island (Peninsular Malaysia); white = Sumatra; hatched = Zoo samples (on top network: Singapore Zoo (H2), Negara Zoo, Kuala Lumpur (H7) and Batu Secret Zoo & Maharani Zoo, Java (H8)).
Fig. 1 in Molecular systematics and biogeography of the Hemigalinae civets (Mammalia, Carnivora)
Fig. 1. Map showing the distribution of the samples of Hemigalinae used in this study. The gray shadings show the range of Chrotogale owstoni Thomas, 1912, Cynogale bennettii Gray, 1837 and Hemigalus derbyanus (Gray, 1837); Diplogale hosei (Thomas, 1892) is only found on Borneo and Macrogalidia musschenbroekii (Schlegel, 1879) only occurs on Sulawesi. The size of the sample symbols corresponds to the number of samples from each area (the smallest equals 1, and the largest equals 12–14).
Fig. 2. Bayesian tree reconstructed from a in Molecular systematics and biogeography of the Hemigalinae civets (Mammalia, Carnivora)
Fig. 2. Bayesian tree reconstructed from a combined dataset of Cytb + ND2 + FGB + IRBP (3342 bp). The values on the branches are bayesian posterior probabilities for the partitioned analysis (see text for models) and bootstrap proportions obtained from ML analysis (model: GTR + I + G).
Fig. 3 in Molecular systematics and biogeography of the Hemigalinae civets (Mammalia, Carnivora)
Fig. 3. Phylogenetic tree obtained with NJ for a fragment of Cytb (893 bp). The values over the branches are the bootstrap proportions for NJ, and below the branches are those for ML. Co = Chrotogale owstoni Thomas, 1912; Hd = Hemigalus derbyanus (Gray, 1837); Dh = Diplogale hosei (Thomas, 1892); Cb = Cynogale bennettii Gray, 1837.
Figure 2 in The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review
Figure 2. Polyploidy scenario suggested by and reproduced from Bonnaud et al. (2004). Updated diploid chromosome numbers (see Table 2) for the various branches are now Nautiloidea 52; Octopoda 56–60; Sepiolida 74; Sepiida 48–112; Myopsida 86–92 (?22-?172).
Figure 6 in The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review
Figure 6. Relationships among Sepiida. (A) Consensus tree based on 12S rRNA, 16S rRNA, cytochrome oxidase subunit II (Bonnaud et al. 2006); (B) maximum likelihood tree of cytochrome oxidase subunit I, cytochrome b and ND5 combined (Yoshida et al. 2010); (C) whole evidence approach using four to ten genes (Lindgren et al. 2012). Trees redrawn from original sources.
Figure 7 in The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review
Figure 7. Relationships within Onychoteuthidae. (A) Neighbour-joining tree based on 16S ribosomal RNA (Bonnaud et al. 1998); (B) maximum likelihood tree of five genes (see text) combined (Lindgren 2010); (C) maximum likelihood tree based on whole evidence approach using four to ten genes (Lindgren et al. 2012). All trees redrawn from original sources. Nomenclature uses systematic revision of Bolstad (2010).
FIGURE 17. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURE 17. Hungarosoma bokori Verhoeff, 1928, female, vulvae (Driny Cave). Vulvae in posterior-ventral view (o = opercula) Not scaled.
FIGURE 19 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURE 19. Distribution of the genus Hungarosoma Verhoeff, 1928. Empty dot: H. inexpectatum, solid dots: H. bokori. Distribution of H. bokori in Slovak-Aggtelek Karst drawn in higher scale.
FIGURE 18. A in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURE 18. A Maximum-Likelihood tree (GTR + G + I model) based on the COI gene and rooted with Polyxenus lagurus. All data—except from H. bokori — were obtained from Genbank. Numbers refer to bootstrap values (1000 replicates). Scale bar = 0.02 substitutions / site. For origin of the H. bokori material, see Table 1.
FIGURES 12 – 14. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURES 12 – 14. Hungarosoma bokori Verhoeff, 1928, male (Abaliget Cave). 12: Antenna. 13: Gonopod complex, anterior view. The right side of pair structures is slightly turned laterally. 14: Gonopods in right lateral view. Abbreviations: Letters a – h signal equivalent structures in both views. Anterior gonopods (legs 8): a = cheirite, b = brush-like arm, c = additive divided arm, d = hyaline process. Posterior gonopods (legs 9): e = gonopod, f = ventral hyaline prominence, g = claw shape process with long seta. Not scaled. Photos: Andrej Mock.
FIGURES 6 – 9. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURES 6 – 9. Hungarosoma bokori Verhoeff, 1928, specimens from the Abaliget Cave, preserved in alcohol (not scaled). 6: Habitus of adult male in lateral view; the cheirites of anterior gonopods are visible. 7: Details of the dorsal part of the male trunk. 8: Ventral side of mid-body segments in detail. 9: Dorsal side of a juvenile of stadium III with the shape of the pleurotergites typical for the genus (all material from the Abaliget Cave, Hungary). Photos: Andrej Mock.
FIGURES 10 – 11. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURES 10 – 11. Hungarosoma bokori Verhoeff, 1928, female from the Driny Cave, scanning electronic microscopy of details of the shape and surface of mid-body segments. 10: Dorsolateral view (left side). 11: A pleurotergite, dorsolateral view in detail. Photos: Andrej Mock & Karel Tajovský.
FIGURE 16. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURE 16. Hungarosoma bokori Verhoeff, 1928, male, gonopods (Abaliget Cave). Right lateral view. Letters a – h signal equivalent structures in both views. Abbreviations: Letters a – h signal equivalent structures in both views. Anterior gonopods (legs 8): a = cheirite, b = brush-like arm, c = additive divided arm, d = hyaline process. Posterior gonopods (legs 9): e = gonopod, f = ventral hyaline prominence, g = claw shape process with long seta.
FIGURES 2 – 5. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology
FIGURES 2 – 5. Hungarosoma bokori Verhoeff, 1928, female, holotype (Abaliget Cave). 2: Head end of the body, right lateral view. 3: Tergite 15, dorsal view. 4: Antenna, lateral view. 5: Discernable vulvae in situ (v), right lateral view. Photos: Jörg Spelda.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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