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Depositordc.contributorGrant, Seth
Funderdc.contributor.otherEuropean Commissionen_UK
Funderdc.contributor.otherWellcome Trusten_UK
Data Creatordc.creatorCizeron, M
Data Creatordc.creatorQiu, Z
Data Creatordc.creatorKoniaris, B
Data Creatordc.creatorGokhale, R
Data Creatordc.creatorKomiyama, N
Data Creatordc.creatorFransén, E
Data Creatordc.creatorGrant, SGN
Date Accessioneddc.date.accessioned2020-04-02T08:19:11Z
Date Availabledc.date.available2020-04-02T08:19:11Z
Citationdc.identifier.citationCizeron, M; Qiu, Z; Koniaris, B; Gokhale, R; Komiyama, N; Fransén, E; Grant, SGN. (2020). Mouse Lifespan Synaptome Atlas dataset [dataset]. University of Edinburgh. Centre for Clinical Brain Sciences. https://doi.org/10.7488/ds/2796.en
Persistent Identifierdc.identifier.urihttp://hdl.handle.net/10283/3603
Persistent Identifierdc.identifier.urihttps://doi.org/10.7488/ds/2796
Dataset Description (abstract)dc.description.abstractHow synapses change molecularly during the lifespan and across all brain circuits is unknown. We analyzed the protein composition of billions of individual synapses from birth to old age on a brain-wide scale in the mouse, revealing a program of changes in the lifespan synaptome architecture spanning individual dendrites to the systems level. Three major phases were uncovered, corresponding to human childhood, adulthood and old age. An arching trajectory of synaptome architecture drives the differentiation and specialization of brain regions to a peak in young adults before dedifferentiation returns the brain to a juvenile state. This trajectory underscores changing network organization and hippocampal physiology that may account for lifespan transitions in intellectual ability and memory, and the onset of behavioral disorders. # Note re dataset title # At the request of the journal publisher, the title of this dataset was updated to "Mouse Lifespan Synaptome Atlas dataset". Previous titles of this dataset: * "Raw data from individual synapses across the mouse brain from birth to 18 months. This dataset was previously titled - Synaptome data with individual synapse parameters, types and subtypes for 10 representative sagittal mouse brain sections across the lifespan"en_UK
Dataset Description (TOC)dc.description.tableofcontents# Software # The dataset is intended for use with the application Synaptome Explorer, whose binaries are provided in https://github.com/SynaptomeMapping/SynaptomeExplorerV2 . # Structure # The data are compressed in eleven separate files (10 datasets and 1 for configuration). The configuration file is required, while the individual datasets are optional. The required file and all other files of interest need to be extracted to the same folder. ## Configuration data ## The file "lifespan_data_common.tar.bz2" contains the essential configuration data: * "masks.json": Delineation hierarchy for all datasets in JSON format; * "masks.png": Color lookup table associated with masks.json; * synaptome_explorer_configs/_any_file_.json: configuration file provided as an argument for execution of the application Synaptome Explorer V2. ## Sections ## Each of the other files, each tarball, contains data pertaining to a particular section (a particular sample). Each dataset represents a single section from a particular age. So the identifiers "PUP109_SG3" etc refer to the experiments. ## Contents of each tarball ## For example GKD073_SG1.tar.bz2 contains: * GKD073_SG1/config.json: imaging configuration for the current dataset. * GKD073_SG1/correction.dds: correction greyscale image as the DDS file format, used by the application for better display of the raw image data. * GKD073_SG1/masks.png: image that stores RGBA-encoded delineation IDs. * GKD073_SG1/montage.dds: low-resolution version of the raw image data. * GKD073_SG1/puncta.hdf5: puncta parameters in the HDF5 format. * GKD073_SG1/puncta_extrema_global_and_per_protein.cache: binary cache file storing the minimum and maximum values for all puncta, globally and by channel. * GKD073_SG1/sparsetex.tex: Raw image data at various levels of detail stored as DDS tiles. * GKD073_SG1/sparsetex.cfgp: Binary configuration data for raw image data. The files are automatically placed in a folder named after the dataset name. Therefore, if "root" is the folder where the configuration files were extracted to, then by extracting GKD073_SG1.tar.bz2 into that folder, there will be a new, populated folder "root/GKD073_SG1". ## Ages ## Each of the files refers to a particular age. The mapping is as follows, in ascending order of age (D: day, W: week, M: month): * PUP109_SG3 : 1D * PUP145_SG2 : 1W * PUP011_SG2 : 2W * PUP068_SG3 : 3W * PUP039_SG1 : 1M * PUP058_SG3 : 2M * GKD348_SG1 : 3M * GKD180_SG2 : 6M * GKD139_SG2 : 12M * GKD073_SG1 : 18Men_UK
Languagedc.language.isoengen_UK
Publisherdc.publisherUniversity of Edinburgh. Centre for Clinical Brain Sciencesen_UK
Relation (Is Referenced By)dc.relation.isreferencedbyhttps://doi.org/10.1126/science.aba3163en_UK
Relation (Is Referenced By)dc.relation.isreferencedby"A brain-wide atlas of synapses across the mouse lifespan" By Mélissa Cizeron, Zhen Qiu, Babis Koniaris, Ragini Gokhale, Noboru H. Komiyama, Erik Fransén, Seth G. N. Grant Published Online11 Jun 2020 DOI: 10.1126/science.aba3163
Supersedesdc.relation.replaceshttps://doi.org/10.7488/ds/2711en_UK
Subjectdc.subjectsynaptomeen_UK
Subjectdc.subjectlifespanen_UK
Subjectdc.subjectsingle-synapseen_UK
Subjectdc.subjectarchitectureen_UK
Subject Classificationdc.subject.classificationNeuroscienceen_UK
Titledc.titleMouse Lifespan Synaptome Atlas dataseten_UK
Alternative Titledc.title.alternativeA lifespan program of mouse synaptome architectureen_UK
Alternative Titledc.title.alternativeRaw data from individual synapses across the mouse brain from birth to 18 months. This dataset was previously titled - Synaptome data with individual synapse parameters, types and subtypes for 10 representative sagittal mouse brain sections across the lifespan
Typedc.typedataseten_UK

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