| dc.contributor |
European Commission |
|
| dc.contributor |
Wellcome Trust |
|
| dc.contributor |
Grant, Seth |
|
| dc.creator |
Cizeron, M |
|
| dc.creator |
Qiu, Z |
|
| dc.creator |
Koniaris, B |
|
| dc.creator |
Gokhale, R |
|
| dc.creator |
Komiyama, N |
|
| dc.creator |
Fransén, E |
|
| dc.creator |
Grant, SGN |
|
| dc.date |
2020-04-02T08:19:11Z |
|
| dc.date |
2020-04-02T08:19:11Z |
|
| dc.date.accessioned |
2023-02-17T20:53:43Z |
|
| dc.date.available |
2023-02-17T20:53:43Z |
|
| dc.identifier |
Cizeron, 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. |
|
| dc.identifier |
https://hdl.handle.net/10283/3603 |
|
| dc.identifier |
https://doi.org/10.7488/ds/2796 |
|
| dc.identifier.uri |
http://localhost:8080/xmlui/handle/CUHPOERS/244139 |
|
| dc.description |
How 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"
# Note re file download #
There is a known issue in Chrome and Microsoft Edge which can cause .bz2 files to download in a corrupted form, where the browser renames the file .zip but the zip file is unusable. If this is affecting you please use a different browser. |
|
| dc.description |
# 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 : 18M |
|
| dc.format |
text/plain |
|
| dc.format |
application/zip |
|
| dc.format |
application/zip |
|
| dc.format |
application/zip |
|
| dc.format |
application/zip |
|
| dc.format |
application/zip |
|
| dc.format |
application/zip |
|
| dc.format |
application/zip |
|
| dc.format |
application/zip |
|
| dc.format |
application/zip |
|
| dc.format |
application/zip |
|
| dc.format |
application/zip |
|
| dc.language |
eng |
|
| dc.publisher |
University of Edinburgh. Centre for Clinical Brain Sciences |
|
| dc.relation |
https://doi.org/10.1126/science.aba3163 |
|
| dc.relation |
"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 |
|
| dc.relation |
https://doi.org/10.7488/ds/2711 |
|
| dc.subject |
synaptome |
|
| dc.subject |
lifespan |
|
| dc.subject |
single-synapse |
|
| dc.subject |
architecture |
|
| dc.subject |
Neuroscience |
|
| dc.title |
Mouse Lifespan Synaptome Atlas dataset |
|
| dc.title |
A lifespan program of mouse synaptome architecture |
|
| dc.title |
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 |
|
| dc.type |
dataset |
|