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RNA-seq dataset for Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism
<p>Data to be used along with <a href="https://github.com/neelroop/asd-development-coexpression-2013">code</a> from 2013 paper that was originally on a site hosted at UCLA, but may no longer be accessible.</p>
Transcriptomic analyses of normal-appearing CNS white matter from multiple sclerosis donors reveal subtype-specific molecular signatures of disease (REVISED)
<p>Datasets of bulk RNA-sequencing of NAWM from MS donors + supplementary images of RNA deconvolution of cell trajectories</p>
Appendix Morphometric parameters of Chaetonotus (Chaetonotus) antrumus Kolicka sp. nov. Abbreviations: N = number of specimens or structures analysed; Range = the smallest and the largest structure measurement found among all specimens measured; SD = standard deviation. All measurements are given in micrometers (μm); all indicators are given as a percentage (%) and italicized. in A new species of freshwater Chaetonotidae (Gastrotricha, Chaetonotida) from Obodska Cave (Montenegro) based on morphological and molecular characters
Appendix Morphometric parameters of Chaetonotus (Chaetonotus) antrumus Kolicka sp. nov. Abbreviations: N = number of specimens or structures analysed; Range = the smallest and the largest structure measurement found among all specimens measured; SD = standard deviation. All measurements are given in micrometers (μm); all indicators are given as a percentage (%) and italicized.
Fig. 1 in Morphology and Molecular Analyses of a New Marine Ciliate, Arcuseries minima sp. nov. (Ciliophora: Urostylidae)
Fig. 1. Arcuseries minima sp. nov. in vivo (A–E) and after protargol impregnation (F, G). (A) Ventral view of a representative specimen. (B, C) Cortical granulation in ventral surface. (D, E) Cortical granulation in dorsal surface, three types of cortical granules: the large (arrow), medium-sized (arrowhead), small (double arrowhead). (F) Ventral view of holotype specimen. (G) Dorsal view of a paratype specimen, arrow indicates a basal body. AZM = adoral zone of membranelles; BC = buccal cirrus; E = endoral; FC = frontal cirri; FTC = frontoterminal cirri; LMC = left marginal cirri; Ma = macronuclear nodules; MC = midventral cirri; Mi = micronuclei; P = paroral; PTC = pretransverse cirri; RMC = right marginal cirri; TC = transverse cirri; 1–3 = dorsal kineties 1–3. Scale bars: 20 µm.
Fig. 3 in Morphology and Molecular Analyses of a New Marine Ciliate, Arcuseries minima sp. nov. (Ciliophora: Urostylidae)
Fig. 3. Maximum likelihood and Bayesian inference analyses based on 18S rDNA sequences. The new sequence provided in the present work is indicated in bold and by a white arrow. Numbers at nodes indicate the bootstrap values of ML out of 1,000 replicates and the posterior probability of BI. Fully supported (100/1.00) branches are marked with solid circles. The scale bar corresponds to 2 substitutions per 100 nucleotide positions.
Fig. 3. Phylogenetic trees obtained from a concatenated dataset with a in Molecular Systematics and Morphological Analyses of the Subgenus Setihenricia (Echinodermata: Asteroidea: Henricia) from Japan
Fig. 3. Phylogenetic trees obtained from a concatenated dataset with a total length of 1,277 bp, consisting of seven mitochondrial genes (16S, tRNA-Ala, tRNA-Leu, tRNA-Asn, tRNA-Gln, tRNA-Pro, and COI). The trees were built based on maximum likelihood (ML, left) and Bayesian inference (BI, right). Values at nodes indicate bootstrap scores from ML and posterior probabilities from BI. Outgroups are only shown in the ML tree with both the support values. Scale bars indicate the number of nucleotide substitutions per site. OTUs sequenced in this study are in bold face. Each letter in parentheses after non-bold OTUs denotes the source: C, Chichvarkhin (2017b); F, Foltz and Rocha- Olivares (unpublished); K, Knott et al. (2018); L, Lopes et al. (2016); M, Matsubara et al. (2004); W, Wada et al. (1996). Circles indicate species listed as Setihenricia in Chichvarkhin and Chichvarkhina (2017). Triangles indicate species morphologically identified as Setihenricia in this study (see Fig. 4A).
Fig. 2 in Molecular Systematics and Morphological Analyses of the Subgenus Setihenricia (Echinodermata: Asteroidea: Henricia) from Japan
Fig. 2. Measurements (morphometrics) of four kinds of ossicles of Henricia nipponica (Oshoro): A, dorsal spine (DS); B, adambulacral spine (AdS); C, adambulacral plate (AdP), proximal view; D, ambulacral plate (AmP), proximal view.
Fig. 5 in Molecular Systematics and Morphological Analyses of the Subgenus Setihenricia (Echinodermata: Asteroidea: Henricia) from Japan
Fig. 5. Side views of the arms of Henricia nipponica (Oshoro) (A, B) and Henricia tumida (C, D). A, C, Lower magnification; B, D, higher magnification of the rectangle on A and C, respectively. The number of the rows of spines on the inferomarginal plate can be interpreted as either two (solid line), two or three (dashed line), or three (dotted line). Scale bars indicate 1 mm.
Fig. 1 in Molecular Systematics and Morphological Analyses of the Subgenus Setihenricia (Echinodermata: Asteroidea: Henricia) from Japan
Fig. 1. Sampling locations of Henricia (circle) and Echinaster (square) specimens around Japan. (1) Off Abashiri, Hokkaido; H. sp. 2 (Abashiri 1), H. sp. 3 (Abashiri 2); (2) Oshoro, Hokkaido; H. nipponica (Oshoro), H. ohshimai (Oshoro); (3) Off Iwanai, Hokkaido; H. reniossa; (4) Akkeshi, Hokkaido; H. reticulata, H. tumida, H. sp. 1 (Akkeshi); (5) Muroran, Hokkaido; H. nipponica (Muroran); (6) Off Iwate; H. hayashii; (7) Off Miyagi; H. kinkasana; (8) Off Fukushima; H. sp. 4 (Fukushima); (9) Misaki, Kanagawa; H. ohshimai (Misaki); (10) Iki Island, Nagasaki; H. regularis; (11) Okinoerabu Island, Kagoshima; H. sp. 8 (Okinoerabu); (12) Iheya Island, Okinawa; E. sepositus; (13) Okinawa Island, Okinawa; H. sp. 5 (Okinawa); (14) Nagannu Island, Okinawa; H. sp. 7 (Nagannu); (15) Aka Island, Okinawa; E. callosus; (16) Miyako Island, Okinawa; H. sp. 6 (Miyako); (17) Iriomote Island, Okinawa; E. luzonicus.
Fig. 4 in Molecular Systematics and Morphological Analyses of the Subgenus Setihenricia (Echinodermata: Asteroidea: Henricia) from Japan
Fig. 4. Morphological characters which might be useful to distinguish Setihenricia species from non-Setihenricia species. A, number of rows of spines on each inferomarginal plate; B, SEM images of AdP; C, AdPwidth; D, SEM images of AmP; E, photographs of entire body; F, ratios of AmPwidth/AmPneck/r. See Table 4for abbreviations. Circles on boxplots (A, C, and F) indicate outliers. Specimens that show three (indicated by a vertical dashed line on A) or more rows of the spines can be identified as Setihenricia (Chichvarkhin and Chichvarkhina 2017). Enlarged images of B, D, and E are available in the figshare repository (Wakita et al. 2019).
Fig. 6 in Molecular Systematics and Morphological Analyses of the Subgenus Setihenricia (Echinodermata: Asteroidea: Henricia) from Japan
Fig. 6. Morphological characters representing the degree of tapering of spines. A, SEM images of DS; B, ratios of DSbase/DStip; C, SEM images of AdS; D, ratios of AdSbase/AdStip. See Table 4for abbreviations. Circles on boxplots (B and D) indicate outliers. On B and D, a value above one (indicated by a vertical dashed line) can be interpreted that the spine is tapered. Enlarged images of A and C are available in the figshare repository (Wakita et al. 2019).
Fig. 5 in First report of molecular taxonomic analyses of European beaver metazoan parasites from Hungary
Fig. 5 Phylogenetic tree of Schizocarpus beaver fur mites and related astigmated mites based on the cytochrome c oxidase subunit I (COI) gene. The tree was generated with the maximum likelihood method and GTR model in MEGA 7.0. Nucleotide sequences obtained in this study are indicated in red. Branch lengths represent the number of substitutions per site inferred according to the scale shown
Fig. 4 in First report of molecular taxonomic analyses of European beaver metazoan parasites from Hungary
Fig. 4 Phylogenetic tree of Stichorchis subtriquetrus beaver fluke and related flukes based on the 18S rRNA gene. The tree was generated with the maximum likelihood method and Kimura model in MEGA 7.0. Nucleotide sequences obtained in this study are indicated in red. Branch lengths represent the number of substitutions per site inferred according to the scale shown
Fig. 3 in First report of molecular taxonomic analyses of European beaver metazoan parasites from Hungary
Fig. 3 Characteristics of Schizocarpus sp. adult male mite from Castor fiber in Hungary, a habitus in ventral view, b ventral opisthosoma with the suckers and the setae, c opisthosoma and the opisthonotal shield, d anterioventral part of the mite with the mouthparts and legs in higher magnification
Fig. 2 in First report of molecular taxonomic analyses of European beaver metazoan parasites from Hungary
Fig. 2 Dorsal and abdominal view of Platypsyllus castoris adult removed from Castor fiber in Hungary
Fig. 1 in First report of molecular taxonomic analyses of European beaver metazoan parasites from Hungary
Fig. 1 Castor fiber trapping sites in Hungary 2017–2021. a Győr-Moson-Sopron county 13 individuals; b Jász-Nagykun-Szolnok county 26 individuals; c Zala county 6 individuals; location; d Veszprém county 2 individuals
Fig. 7. Acetes spiniger Hansen, 1919 in Taxonomic Assessment of Acetes indicus H. Milne Edwards, 1830 (Crustacea, Decapoda, Sergestoidea) as Revealed from Molecular and Morphological Analyses: Re-validation of A. spiniger Hansen, 1919 and Designation of a New Species
Fig. 7. Acetes spiniger Hansen, 1919. (a–e) male (cl 4.3 mm) and (f–i) female (cl. 5.8 mm) from off Kuala Selangor, Malaysia (NSMT-Cr 31637): a, anterior part of cephalothorax, lateral; b, posterior part of abdomen, lateral; c, right left lower antennular flagellum; d, basal segments of third pereopod and genital coxa, ventral; e, capitulum of right petasma; f, anterior part of cephalothorax, lateral; g, basal segments of third pereopod and third and fourth thoracic sternites, ventral; h, lateral profile showing channels and sternites between third and fourth thoracic somites, i, posterior part of telson, dorsal. Abbreviations: gc, genital coxa; iiist, ivst, third and fourth thoracic sternites, respectively.
Fig. 6 in Taxonomic Assessment of Acetes indicus H. Milne Edwards, 1830 (Crustacea, Decapoda, Sergestoidea) as Revealed from Molecular and Morphological Analyses: Re-validation of A. spiniger Hansen, 1919 and Designation of a New Species
Fig. 6. Acetes omorii Hanamura, Imai & Hardianto sp. nov. (a) holotype male (cl 5.3 mm) (NSMT-Cr 31621), and (b–d) paratype female (cl 6.0 mm) (NSMT-Cr 31622) from Matang Mangrove, Malaysia: a, b, right lower antennular flagellum of male and female, respectively; c, basal segments of third pereopod and third and fourth abdominal sternites, ventral; d, lateral profile showing channels and sternites between third and fourth thoracic somites. Abbreviations: iiist, ivst, third and fourth thoracic sternites, respectively.
Fig. 3 in Taxonomic Assessment of Acetes indicus H. Milne Edwards, 1830 (Crustacea, Decapoda, Sergestoidea) as Revealed from Molecular and Morphological Analyses: Re-validation of A. spiniger Hansen, 1919 and Designation of a New Species
Fig. 3. Map showing sampling localities and distribution ranges of Acetes indicus, A. omorii sp. nov. and A. spiniger recognised in this study with certainty: blue solid circles (nos. 1–2) for A. indicus, green solid squares and open square (museum vouchered specimens) for A. spiniger, and red solid triangles for A. omorii sp. nov. Numerals indicating sampling locations: 1, Chiringa; 2, Kumira-Sandwip Ship Ghat; 3, Merbok Mangrove; 4; Matang Mangrove, 5; Kuala Selangor; 6, Malacca; 7, Samut Prakan; 8, Setarap Estuary, South Kalimantan; and 9, Goa.
Fig. 2 in Taxonomic Assessment of Acetes indicus H. Milne Edwards, 1830 (Crustacea, Decapoda, Sergestoidea) as Revealed from Molecular and Morphological Analyses: Re-validation of A. spiniger Hansen, 1919 and Designation of a New Species
Fig. 2. Haplotype network (implemented in PopART) of the Acetes indicus, A. omorii sp. nov., and A. spiniger based on the mitochondrial 16S (a) and mitochondrial COI (b) markers using minimum spanning network (MSN) analysis with outgroups of congeneric species. Circles with different colours represent different species.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.