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35 results for “Breakpoint”
Marcell Experimental Forest breakpoint streamflow, 1962 - ongoing
This data publication contains breakpoint streamflow data collected from 1962-ongoing at the Marcell Experimental Forest (MEF) in Itasca County, Minnesota, which is operated and maintained by the USDA Forest Service, Northern Research Station. The MEF was formally established in 1962 and contains six watersheds instrumented for hydrologic monitoring, each consisting of an upland portion and a peatland that is the source of a stream leaving the watershed. The watersheds and environmental monitoring at the MEF are part of a long-term research program on the hydrology and biogeochemistry of watersheds with uplands and northern peatlands.
HGT breakpoints and events detected by LocalHGT in 2098 real data
<p> </p> <table> <tbody> <tr> <td>filter_hgt_results.zip</td> <td>the HGT breakpoints of all samples, in this folder, each CSV file represents a sample. </td> </tr> <tr> <td>identified_event.csv</td> <td>the HGT events of all samples, the results of all samples are in this file.</td> </tr> <tr> <td>TableS1</td> <td>phenotypes of all samples</td> </tr> <tr> <td>use.zip</td> <td>Microbial abundances of all samples, in this folder, all samples from the same cohort are in a single file.</td> </tr> </tbody> </table> <p> </p>
Dataset supporting the tool 'delfies: a Python package for the detection of DNA breakpoints with neo-telomere addition'
<h2>Purpose</h2> <p><br>These data can be used to test my tool <a href="https://github.com/bricoletc/delfies">delfies </a>on real data, to get a concrete sense of its inputs/outputs and test that it is <br>properly installed.</p> <h2>Description</h2> <h3>Genome</h3> <p>I downloaded the genome of <em>Oscheius onirici</em>, accession: <a href="https://www.ebi.ac.uk/ena/browser/view/GCA_932521025.1">GCA_932521025</a>.</p> <p>I subsampled the genome to the last 2kbp of chromosome I, which contains an elimination breakpoint, <br>using `seqkit` v2.8.2, giving the FASTA file in this release.</p> <h3>Sequencing data</h3> <p>I then downloaded the following sequencing data for *O. onirici*, from the European Nucleotide Archive:</p> <ul> <li>ERR5967937: Illumina NovaSeq 6000 paired end short reads. Reads are 2x150bp with average per-base quality of Q27.</li> <li>ERR10796202: Oxford Nanopore PromethION long reads. Reads have average length 11.9kbp and average per-base quality Q11.4.</li> <li>ERR7979900: Pacific Biosciences (PacBio) Sequel II long reads. Reads have average length 11.1kbp and average per-base quality Q28.<br><br></li> </ul> <p>And aligned them to the above genome with `minimap2` version 2.26-r1175, using the following presets: <br>"map-ont" for the Nanopore data, "map-hifi" for the PacBio data, "sr" for the Illumina data.</p> <p>After sorting with `samtools`, this gives the BAM files in this release.</p> <h3>Running delfies</h3> <p>I then ran `delfies` version 0.6.0 on each BAM and genome, as:</p> <p>```sh<br>delfies --threads 16 \<br> --telo_forward_seq TTAGGC \<br> --breakpoint_type all \<br> --min_mapq 20 \<br> --min_supporting_reads 6 \<br> \${genome} \${bam} \${odirname}<br>```</p> <p>The three resulting output directories are in this release, prefixed with `delfies_`.</p> <p><strong>A single, identical breakpoint is found using all three BAMs</strong> (see files '*breakpoint_locations.bed').</p> <h3>Data source</h3> <p>The above raw data were produced and released by the Wellcome Sanger Institute as part of projects <br><a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB51305">PRJEB51305</a> and <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB59023">PRJEB59023.</a></p>
Mapping breakpoint types: an exploratory study
<p>This repository contains the breakpoint types study dataset.</p> <p><strong>Abstract</strong></p> <p>Debugging is a relevant task for finding bugs during software development, maintenance, and evolution. During debugging, developers use modern IDE debuggers to analyze variables, step execution, and set breakpoints. Observing IDE debuggers, we find several breakpoint types. However, what are the breakpoint types? The goal of our study is to map the breakpoint types among IDEs and academic literature. Thus, we mapped the gray literature on the documentation of the nine main IDEs used by developers according to the three public rankings. In addition, we performed a systematic mapping of academic literature over 68 articles describing breakpoint types. Finally, we analyzed the developers understanding of the main breakpoint types through a questionnaire. We present three main contributions: (1) the mapping of breakpoint types (IDEs and literature), (2) compiled definitions of breakpoint types, (3) a breakpoint type taxonomy. Our contributions provide the first step to organize breakpoint IDE taxonomy and lexicon, and support further debugging research.</p>
Vegetation greenesss data for the Aït Benhaddou Catchment, Morocco. Includes: 1984-2019 NDVI time series, breakpoint analysis results, and resillience indicator results, among others.
<p>This dataset is comprised of two main parts, both originating from different but related works. </p> <p>The NDVI timeseries and breakpoint analysis were originally developed by Vermeer (2021) for the MSc thesis: Vermeer, A. L. (2021). <em>Ecological stability in the face of climatic disturbances: a case study of a dryland ecosystem in the Moroccan High Atlas Mountains</em>. These data include a harmonized timeseries of Normalized Difference Vegetation Index from different Landsat missions at 30x30 meter resolution for the Aït Benhaddou catchment in Morocco. It also includes the output of a breakpoint analysis that was conducted using this dataset, which showcases different statistical breakpoints in NDVI after a severe drought that occured between 1998 and 2002. Shapefiles, a DEM and masks of irrigiated areas for the catchment are also included. For more information about these data, consult Vermeer (2021).</p> <p>The secondary part of this dataset was produced by Grootoonk (2024) for the MSc thesis: Grootoonk, W. (2024). <em>Relations between temporal resilience indicators and trend breakpoints in a dryland high-mountain catchment, </em>drawing upon the original dataset from Vermeer (2021). These data include Kendall's tau values for the resillience indicators variance and lag-one autocorrelation, computed using a rolling window for each pixel. Results for differerent window sizes (WS) for both indicators are included. </p> <p>Beyond these main results, a number of additional data sources are provided. These are Kendall's tau for precipitation variance in the area, produced using CHIRPS data (https://www.chc.ucsb.edu/data/chirps) and a NSI soil salinity map produced from Landsat imagery. See Grootoonk (2024) for more information. </p>
QC and WGS around the breakpoints of deletions in the compound heterozygous PRKN-deficient PD iPSC line FINi006-A (FI.CS.PRKNDex2/Dex5-7.@40)
<p>BAM files from WGS on the regions of deletions in both <em>PRKN</em> gene alleles of the iPSC line (clone 18) derived using Sendai virus from PRKN 09/090 patient's fibroblasts </p>
Results for trend and breakpoint analyses from: Losing flow in free-flowing, Mediterranean-climate streams
<p>Stream drying is happening globally, with significant ecological and social consequences. Most examples of stream drying come from systems influenced by dam operations or those with highly exploited aquifers. Stream drying is also thought to be happening due to climate change, but examples are surprisingly limited. We explored flow trends from the five Mediterranean-climate regions with a focus on unregulated streams with long-term gauge records. We found consistent evidence of decreasing discharge trends, increasing zero-flow days, and steeper downward discharge trends in smaller basins. Beyond directional trends, many systems recently shifted flow state, including some streams that shifted from perennial to intermittent flow states. Our analyses provide evidence of stream drying consistent with climate change, but also highlight knowledge gaps and challenges in empirically and statistically documenting flow regime shifts. We discuss the myriad consequences of losing flow and propose strategies for improving detection and adapting to flow change.</p>
Data from: The role of breakpoint mutations, supergene effects, and ancient nested rearrangements in the evolution of adaptive chromosome inversions in the yellow monkey flower, Mimulus guttatus
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Breakpoint phenological responses in high-Arctic arthropods
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Results for trend and breakpoint analyses from: Losing flow in free-flowing Mediterranean-climate streams
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Detection of fusion transcripts and their genomic breakpoints from RNA sequencing data - Table S03 - All detected SVs.xlsx
<p>Large concatenated results table on all samples of the Dr. Disco study.</p> <p> </p>
Data from: Multiple large inversions and breakpoint rewiring of gene expression in the evolution of the fire ant social supergene
Supergenes consist of co-adapted loci that segregate together and are associated with adaptive traits. In the fire ant Solenopsis invicta, two 'social' supergene variants regulate differences in colony queen number and other traits. Suppressed recombination in this system is maintained, in part, by a >9 Mb inversion, but the supergene is larger. Has the supergene in S. invicta undergone multiple large inversions? The initial gene content of the inverted allele of a supergene would be the same as that of the wild-type allele. So, how did the inversion increase in frequency? To address these questions, we cloned one extreme breakpoint in the fire ant supergene. In doing so, we found a second large (>800 Kb) rearrangement. Furthermore, we determined the temporal order of the two big inversions based on the translocation pattern of a third small fragment. Because the S. invicta supergene lacks evolutionary strata, our finding of multiple inversions may support an introgression model of the supergene. Finally, we showed that one of the inversions swapped the promoter of a breakpoint-adjacent gene, which might have conferred a selective advantage relative to the non-inverted allele. Our findings provide a rare example of gene alterations arising directly from an inversion event.
Breakpoint Analysis of de Novo Apparently Balanced Chromosomal Translocations
ClinicalTrials.gov study NCT01826708. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Treatment of Breakpoint Cluster Region-Abelson (BCR-ABL) Negative ALL in Adults
ClinicalTrials.gov study NCT04179929. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Multiple large inversions and breakpoint rewiring of gene expression in the evolution of the fire ant social supergene
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Data from: Postglacial colonization routes coincide with a life history breakpoint along a latitudinal gradient
While adaptive divergence along environmental gradients has repeatedly been demonstrated, the role of postglacial colonization routes in determining phenotypic variation along gradients has received little attention. Here we used a hierarchical QST-FST approach to separate the roles of adaptive and neutral processes in shaping phenotypic variation in moor frog (Rana arvalis) larval life-histories along a 1700 km latitudinal gradient across northern Europe. This species has colonized Scandinavia via two routes with a contact zone in northern Sweden. By using neutral SNP and common garden phenotypic data from 13 populations at two temperatures, we showed that most of the variation along the gradient occurred between the two colonizing lineages. We found little phenotypic divergence within the lineages, however, all phenotypic traits were strongly diverged between the southern and northern colonization routes, with higher growth and development rates and larger body size in the north. The QST estimates between the colonization routes were four times higher than FST, indicating a prominent role for natural selection. QST within the colonization routes did not generally differ from FST, but we found temperature-dependent adaptive divergence close to the contact zone. These results indicate that lineage-specific variation can account for much of the adaptive divergence along a latitudinal gradient.
Data from: Intrachromosomal rearrangements in avian genome evolution: evidence for regions prone to breakpoints
It is generally believed that the organization of avian genomes remains highly conserved in evolution as chromosome number is constant and comparative chromosome painting demonstrated there to be very few interchromosomal rearrangements. The recent sequencing of the zebra finch (Taeniopygia guttata) genome allowed an assessment of the number of intra-chromosomal rearrangements between it and the chicken (Gallus gallus) genome, revealing a surprisingly high number of intra-chromosomal rearrangements. With the publication of the turkey (Meleagris gallopavo) genome it has become possible to describe intrachromosomal rearrangements between these three important avian species, gain insight into the direction of evolutionary change and assess whether breakpoint regions are reused in birds. To this end, we aligned entire chromosomes between chicken, turkey and zebra finch, identifying syntenic blocks of at least 250kb. Potential optimal pathways of rearrangements between each of the three genomes were determined, as was a potential Galliform ancestral organization. From this, our data suggest that around one third of chromosomal breakpoint regions may recur during avian evolution, with 10% of breakpoints apparently recurring in different lineages. This agrees with our previous hypothesis that mechanisms of genome evolution are driven by hotspots of non-allelic homologous recombination.
GCB-Breakpoint-Summary
<p>Primary data used to create figures and tables</p>
Data from: Intrachromosomal rearrangements in avian genome evolution: evidence for regions prone to breakpoints
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Data from: Postglacial colonization routes coincide with a life history breakpoint along a latitudinal gradient
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.