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DNA methylation in sperm of rats at two ages exposed or not to 2,2',4,4'-tetrabromodiphenyl ether
<p><strong>Introduction</strong></p> <p>This study was designed to determine the potential of environmentally relevant levels of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) to induce age-dependent changes in a rat’s sperm epigenome. The methods used to generate the files are described below.</p> <p> </p> <p><strong>Experimental design</strong></p> <p>Twelve seven-week-old pregnant Wistar rats were divided into two groups (6 per group) – control and BDE-47 exposed group. Between pregnancy day 8 and postnatal day 21 (PND21), dams in each group were fed from the tip of pipette 0.2 µL/g body weight of the vehicle (tocopherol-stripped corn oil) or the same volume of a 1 mg/mL solution of BDE-47 daily. The BDE-47 group resulted in an exposure level of 0.2 mg/kg body weight of BDE-47 per day. On PND65 and PND120, one male pup randomly selected from each litter was euthanized, and epididymal motile spermatozoa were collected via the swim-up procedure as described in detail elsewhere (Suvorov et al., 2018). Sperm DNA was extracted using the rapid method (Wu et al., 2015). Extracted sperm DNA was subjected to reduced representation bisulfite sequencing (RRBS).</p> <p> </p> <p><strong>Reduced representation bisulfite sequencing</strong></p> <p>For RRBS, bisulfite-converted libraries were prepared from 100 ng of the sperm DNA using Ovation RRBS Methyl-Seq System and EpiTect Fast DNA Bisulfite Kit (Cat. #59824, Qiagen) following manufacturers’ protocols. Sequencing of libraries was done using the HiSeq 2500 sequencing system (Illumina) in Deep Sequencing Core Facility of the University of Massachusetts Medical School (Schrewsbury, MA) with an average of 18.0 million unique reads per sample.</p> <p> </p> <p><strong>Bioinformatic analysis</strong></p> <p>Raw reads from the sequence were processed following the recommended protocol for libraries prepared with Ovation RRBS Methyl-Seq System (NuGEN) and then mapped to the rn6 Rattus norvegicus reference genome using Bismark (version 0.16.1) and bowtie-2 (version 2.2.9). PCR duplicates were removed using nudup.py (version 2.2). The resulting SAM files for the control and BDE-47 group for the two ages, PND65 and 120 are uploaded. </p> <p> </p>
Operating diagram of hatching module, this module consists of two clearly separated sections, each consisting of two long tanks (2 × 0.2 × 0.2 m) designed to accommodate hatching boxes, a filtration tank and an independent water circulation pump with a cooling unit and UV sterilizer. This allows simultaneous monitoring of 16 batches of eggs. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of hatching module, this module consists of two clearly separated sections, each consisting of two long tanks (2 × 0.2 × 0.2 m) designed to accommodate hatching boxes, a filtration tank and an independent water circulation pump with a cooling unit and UV sterilizer. This allows simultaneous monitoring of 16 batches of eggs.
Operating diagram of IF incubator, two identical incubators were used for eggs that were already sorted. They are made up of an isothermal enclosure and contain three tiers (100 × 60 × 17 cm). The water circulating in each tier comes from the same filtration, cooling and sterilisation device. As a result, the eggs placed in the different tiers are subject to the same temperature regime. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of IF incubator, two identical incubators were used for eggs that were already sorted. They are made up of an isothermal enclosure and contain three tiers (100 × 60 × 17 cm). The water circulating in each tier comes from the same filtration, cooling and sterilisation device. As a result, the eggs placed in the different tiers are subject to the same temperature regime.
Top view of DR1/DR2 double riffle, each section contains a spawning ground made up of eight gravel-filled trays, a rest area. The "double riffle" was designed to accommodate two groups from 25 to 50 specimens of broodstock in strictly identical conditions. The spawning grounds are equipped with waterproof, motion-sensing cameras with infrared night vision, connected to a 1000 Gb recorder. The diurnal and nocturnal activities of the two groups can therefore be simultaneously recorded over a long period. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Top view of DR1/DR2 double riffle, each section contains a spawning ground made up of eight gravel-filled trays, a rest area. The "double riffle" was designed to accommodate two groups from 25 to 50 specimens of broodstock in strictly identical conditions. The spawning grounds are equipped with waterproof, motion-sensing cameras with infrared night vision, connected to a 1000 Gb recorder. The diurnal and nocturnal activities of the two groups can therefore be simultaneously recorded over a long period.
Operating diagram of DR1/DR2 double riffle; it consists of two independent sections (DR1 and DR2), each containing 630 litres of water and measuring 2.5 x 0.6 m. Each section contains a filtration system separate from the fish, a cooling unit and an ultraviolet sterilizer. An 80 W UQL lamp completes the lighting of the module lit during the day. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of DR1/DR2 double riffle; it consists of two independent sections (DR1 and DR2), each containing 630 litres of water and measuring 2.5 x 0.6 m. Each section contains a filtration system separate from the fish, a cooling unit and an ultraviolet sterilizer. An 80 W UQL lamp completes the lighting of the module lit during the day.
Operating diagram of the incubator, two tiered modules contain six independent incubators. Three shallow hatching are (220 × 60 × 17 cm) stacked on top of each other to create a compact assembly in which each tier functions independently. Eighteen trays covered with eggs can be placed in each tier, allowing the simultaneous incubation of seven to nine lays. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of the incubator, two tiered modules contain six independent incubators. Three shallow hatching are (220 × 60 × 17 cm) stacked on top of each other to create a compact assembly in which each tier functions independently. Eighteen trays covered with eggs can be placed in each tier, allowing the simultaneous incubation of seven to nine lays.
Fig.1 in Two new cocoon-forming beetles (Coleoptera: Cucujoidea: Bothrideridae) from Baltic amber
Fig.1. The Baltic amber Pseudobothrideres, reconstructions: A – P. rugiorum sp.nov.; B – P.criwecriwayto sp.nov.
Figure 8 in Population and reproductive biology of two caprellid species (Crustacea: Amphipoda) associated to Sargassum cymosum (Phaeophyta: Fucales) on the southeast coast of Brazil
Figure 8. Frequency of females (F), males (M), ovigerous females (OF), mature females (MF) and juveniles (J) in size classes (total length in mm) of Pseudaeginella montoucheti over the studied period.
Figure 6 in Population and reproductive biology of two caprellid species (Crustacea: Amphipoda) associated to Sargassum cymosum (Phaeophyta: Fucales) on the southeast coast of Brazil
Figure 6. Monthly values of ovigerous female density (ind./g of algae) (mean ± standard error) of Paracaprella tenuis and Pseudaeginella montoucheti from October 2010 to September 2011.
Figure 7 in Population and reproductive biology of two caprellid species (Crustacea: Amphipoda) associated to Sargassum cymosum (Phaeophyta: Fucales) on the southeast coast of Brazil
Figure 7. Frequency of females (F), males (M), ovigerous females (OF), mature females (MF) and juveniles (J) in size classes (total length in mm) of Paracaprella tenuis over the studied period.
Fig. 3 in Two fossil species of Petaliini White (Coleoptera: Ptinidae: Dorcatominae) from Eocene Baltic amber
Fig. 3. Petalium widewuto sp. nov., holotype, 6783 [MAIG], habitus: A – ventral view; B – dorsolateral view
Fig. 2 in Two fossil species of Petaliini White (Coleoptera: Ptinidae: Dorcatominae) from Eocene Baltic amber
Fig. 2. Petalium bruteno sp. nov., paratype, 6782 [MAIG], habitus: A – dorsal view; B – ventral view
Fig. 1 in Two fossil species of Petaliini White (Coleoptera: Ptinidae: Dorcatominae) from Eocene Baltic amber
Fig. 1. Petalium bruteno sp. nov., holotype, 6781 [MAIG], habitus: A – dorsal view; B – ventral view
Fig. 6 in Two new Malthodes and a new Podistra from Eocene Baltic amber (Coleoptera, Cantharidae)
Fig. 6. Malthodes (Libertimalthodes) jaredi sp. nov. INHSP-18002 in Baltic amber. A-B: Holotype, lateral views, bars = 0.5 mm
Fig. 4 in Two new Malthodes and a new Podistra from Eocene Baltic amber (Coleoptera, Cantharidae)
Fig. 4. Malthodes (Libertimalthodes) headsi sp. nov. INHSP-18001 in Baltic amber. Holotype, detail of legs, bar = 0.2 mm
Fig. 3 in Two new Malthodes and a new Podistra from Eocene Baltic amber (Coleoptera, Cantharidae)
Fig. 3. Malthodes (Libertimalthodes) headsi sp. nov. INHSP-18001 in Baltic amber. Holotype, dorso-lateral view, bar = 1.0 mm
Fig. 2 in Two new Malthodes and a new Podistra from Eocene Baltic amber (Coleoptera, Cantharidae)
Fig. 2. Podistra (Pseudoabsidia) guthriei sp. nov. INHSP-18000 in Baltic amber. Holotype, detail of elytral apex and last tergites, bar = 0.2 mm
Fig. 7 in Two new Malthodes and a new Podistra from Eocene Baltic amber (Coleoptera, Cantharidae)
Fig. 7. Malthodes (Libertimalthodes) jaredi sp. nov. INHSP-18002 in Baltic amber. Holotype, detail of last sternites, bar = 0.2 mm
Fig. 1 in Two new Malthodes and a new Podistra from Eocene Baltic amber (Coleoptera, Cantharidae)
Fig. 1. Podistra (Pseudoabsidia) guthriei sp. nov. INHSP-18000 in Baltic amber. A: Holotype, dorso-lateral view, bar = 1.0 mm; B: Holotype, ventro-lateral view, bar = 1.0 mm.
Fig. 21 in Integrative taxonomy supports two new species of Macrobiotus (Tardigrada: Eutardigrada: Macrobiotidae) allowing further discussion on the genus phylogeny
Fig. 21. Bayesian phylogenetic reconstruction of Superclade I of the family Macrobiotidae. Values at nodes are BI posterior probability supports, nodes with support <0.70 were collapsed whereas nodes with maximum support values (1.00) are not shown. Newly sequenced taxa are bolded and marked with red font. The scale bar represents substitutions per position.
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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.