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291 results for “C57BL/6J”
ONT direct RNA sequencing Fast5 files from mouse embryonic stem cell (C57BL/6J x CAST/EiJ) - Rep2 (run4-2)
<p>We present a novel approach that leverages Oxford Nanopore direct RNA sequencing technology to detect allele-biased patterns of N6-methyladenosine (m6A) modifications in native mRNAs. Our approach utilized human and mouse cells with known genetic variants to ascertain allelic origin of each mRNA molecule. We employed a supervised machine learning model to detect read-level modification ratios, providing a comprehensive understanding of allele-specific m6A modification (ASM) patterns. To analyze the effects of allele specific m6A modification in mouse, we used hybrid mosue embryonic stem cells (C57BL/6J x CAST/EiJ). This page contains replicate 2 (run 4-2; the files are splited two two parts because of limitations of file size).</p>
ONT direct RNA sequencing Fast5 files from mouse embryonic stem cell (C57BL/6J x CAST/EiJ) - Rep2 (run4-1)
<p>We present a novel approach that leverages Oxford Nanopore direct RNA sequencing technology to detect allele-biased patterns of N6-methyladenosine (m6A) modifications in native mRNAs. Our approach utilized human and mouse cells with known genetic variants to ascertain allelic origin of each mRNA molecule. We employed a supervised machine learning model to detect read-level modification ratios, providing a comprehensive understanding of allele-specific m6A modification (ASM) patterns. To analyze the effects of allele specific m6A modification in mouse, we used hybrid mosue embryonic stem cells (C57BL/6J x CAST/EiJ). This page contains replicate 2 (run 4-1; the files are splited two two parts because of limitations of file size).</p>
Targeted lipidomics yields changes in both arachidonic acid and linoleic acid pathways observed in C57BL/6J mice compared to KitW-sh mice after nitrogen mustard exposure
<p>Sulfur mustard (SM) has been widely used as a chemical warfare agent including most recently in Syria. Mice exposed to SM exhibit an increase in pro-inflammatory cytokines followed by immune cell infiltration in the lung, however, the mechanisms leading to these inflammatory responses has not been completely elucidated. Mast cells are one of the first responding innate immune cells found at the mucosal surfaces of the lung and have been reported to be activated by SM in the skin. Therefore, we hypothesized that nitrogen mustard (NM: a surrogate for SM) exposure promotes activation of mast cells causing chronic respiratory inflammation. To assess the role of mast cells in NM-mediated pulmonary toxicity, we compared the effects of NM exposure between C57BL/6 and B6.Cg-KitW-sh/HNihrJaeBsmJ (Kit<sup><em>W-s</em></sup><sup>h</sup>; mast cell deficient) mice. Lung injury was observed in C57BL/6J mice following NM exposure (0.125 mg/kg) at 72 h, which was significantly abrogated in Kit<sup><em>W-s</em></sup><sup>h</sup> mice. Although both strains exhibited damage from NM, C57BL/6J mice had higher inflammatory cell infiltration and more elevated prostaglandin D<sub>2</sub> (PGD<sub>2</sub>) present in bronchoalveolar lavage fluid compared with Kit<sup><em>W-s</em></sup><sup>h</sup> mice. Additionally, we utilized murine bone marrow-derived mast cells to assess NM-inducedearly and late activation. Although NM exposure did not result in mast cell degranulation, we observed an upregulation in PGD<sub>2</sub> and IL-6 levels following exposure to NM. Results suggest that mast cells play a prominent role in lung injury induced by NM and may contribute to the acute and potentially long-term lung injury observed caused by SM.</p>
Bouts of rest and physical activity in C57BL/6J mice
<p>The objective was to exploit the raw data output from a scalable home cage (type IIL IVC) monitoring (HCM) system (DVC®), to characterize the pattern of undisrupted rest and physical activity (PA) of C57BL/6J mice. The system's tracking algorithm shows that mice in isolation spend 67% of the time in bouts of long rest (≥40s) and 59% of the time was interpreted as sleep. Twenty percent is physical activity (PA), split equally between local movements and locomotion. Decomposition revealed that a day contains ~6500 discrete bouts of short and long rest, and local and locomotor movements. Mice travel ~330m per day, mainly during the dark hours, while travelling speed is similar through the light-dark cycle. Locomotor bouts are usually <0.2m and <1% are >1m. Tracking also revealed fits of abnormal behaviour. The starting positions of the bouts showed no preference for the rear over the front of the cage floor, while there was a strong bias for the peripheral (75%) over the central floor area. The composition of bouts has a characteristic circadian pattern, however, intrusive husbandry routines increased bout fragmentation by ~40%.</p> <p>Extracting electrode activations density (EAD) from the raw data yielded results close to those obtained with the tracking algorithm, with 59% of the time in long rest (<1 EAD s-1) and 20% in PA. We confirm that EAD correlates closely with movement distance (rs>0.95) and the data agreed in ~96% of the file time. Thus, albeit EAD is less informative, it may serve as a proxy for PA and rest, enabling monitoring group-housed mice. The data show that a change in housing density from one to two, and up to three mice had the same effect size on EAD (~2) with no difference between sexes. The EAD deviated significantly from this stepwise increase with 4 mice per cage, suggesting a crowdedness stress inducing sex-specific adaptations.</p> <p>We conclude that informative metrics on rest and PA can be automatically extracted from the raw data flow in near-real time (< 1 hrs). These metrics relay useful longitudinal information to those who use or care for the animals.</p>
Photographs of 15-day wound closure progress in C57BL/6J mice
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Bouts of rest and physical activity in C57BL/6J mice
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Targeted lipidomics yields changes in both arachidonic acid and linoleic acid pathways observed in C57BL/6J mice compared to KitW-sh mice after nitrogen mustard exposure
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Data from: Towards large scale automated cage monitoring – Diurnal rhythm and impact of interventions on in-cage activity of C57BL/6J mice recorded 24/7 with a non-disrupting capacitive-based technique
Abstract Background and aims Automated recording of laboratory animal's home cage behavior is receiving increasing attention since such non-intruding surveillance will aid in the unbiased understanding of the normal animal cage behavior potentially improving animal experimental reproducibility. Material and methods Here we investigate activity of group held (5 mice/cage) female C57BL/6J mice (mus musculus) housed in standard Individually Ventilated Cages (IVC cages) across three test-sites: Consiglio Nazionale delle Ricerche (Rome, Italy), The Jackson Laboratory (Bar Harbor, USA) and Karolinska Insititutet (Stockholm, Sweden). Additionally, comparison of female and male C57BL/6J mice was done at KI. Activity was recorded using a capacitive-based sensor placed non-intrusively on the cage rack under the home cage collecting activity data every 250 msec, 24/7. The data collection was analyzed using non-parametric rank-based analysis of variance (nparLD) for longitudinal data comparing sites, weekdays and sex. Results The system detected an increase in activity preceding and peaking around lights-on followed by a decrease to a rest pattern. At lights off, activity increased substantially displaying a distinct temporal variation across this period. We also documented impact on mouse activity that standard animal handling procedures have, e.g. cage-changes, and show that even simple procedures are stressors impacting in-cage activity. These key observations replicated across the three test-sites, however, it is also clear that, apparently minor local environmental differences generate significant behavioral variances between the sites and within sites across weeks. Comparison of gender revealed differences in activity in the response to cage-change lasting for days in male but not female mice; and apparently also impacting the response to other events such as lights-on in males. Females but not males showed a larger tendency for week-to-week variance in activity possibly reflecting estrous cycling. Conclusions These data demonstrate that real-time home cage monitoring is scalable and run in real time, providing complementary information for animal welfare measures, experimental design and phenotype characterization.
Data from: Towards large scale automated cage monitoring – Diurnal rhythm and impact of interventions on in-cage activity of C57BL/6J mice recorded 24/7 with a non-disrupting capacitive-based technique
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Next Generation Sequencing of Wild-Type C57BL/6J Mouse Cardiac Polyadenylated RNA
GEO Series GSE55788. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Aging-associated changes in gene expression of the lung tissue of the National Center for Geriatrics and Gerontology (NCGG) C57Bl/6J mice
GEO Series GSE209891. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Microarray analysis of gene expression in the livers of C57BL/6J mice fed a choline- and folate-deficient diet
GEO Series GSE96936. Mus musculus. 6 samples. Type: Expression profiling by array.
Adropin transgenesis improves recognition memory in diet-induced obese LDLR-deficient C57BL/6J mice
GEO Series GSE185734. Mus musculus. 24 samples. Type: Expression profiling by high throughput sequencing.
Next Generation Sequencing of Wild-Type C57BL/6J and FVB/NJ Mouse Cardiac Polyadenylated RNA and Small RNA
GEO Series GSE55792. Mus musculus. 111 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
RNA sequencing on liver samples from wild type C57BL/6J mice exposed to the vandetanib
GEO Series GSE284661. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Liver effects of Aflatoxin B1 (AFB1) in wild type (C57BL/6J) and hepatitis C virus-transgenic (HCV-Tg) mice
GEO Series GSE26838. Mus musculus. 20 samples. Type: Expression profiling by array.
RNA sequencing of Tie2 (TEK) silencing in Tie2+ Fibrolast like cells (TF) from the aorta of wild type C57Bl/6J mice.
GEO Series GSE187844. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
Alcohol-free fermented berry beverage phenolics attenuate diet-induced obesity and blood glucose in C57BL/6J mice
GEO Series GSE74008. Mus musculus. 24 samples. Type: Expression profiling by array.
Differential expression of genes in pancreatic islets from high fat fed AKR/J and C57Bl/6J
GEO Series GSE10639. Mus musculus. 8 samples. Type: Expression profiling by array.
Gene expression profiling of C57BL/6J wildtype and IFNAR1 knockout mice following LPS and IFNβ stimulation
GEO Series GSE134549. Mus musculus. 32 samples. Type: Expression profiling by array.
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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.