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-# Comparative microelectrode array dataset of functional development of human PSC-derived and rat neuronal networks
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-## Summary
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-We provide two electrophysiological datasets recorded via a 10-by-10 multi-electrode array chronically implanted in the motor cortex of two macaque monkeys during an instructed delayed reach-to-grasp task ([Brochier et al., 2018](http://doi.org/10.1038/sdata.2018.55)). The datasets contain the continuous measure of extracellular potentials at each electrode sampled at 30 kHz, the local field potentials sampled at 1 kHz and the timing of the online and offline extracted spike times. It also includes the timing of several task-related and behavioral events recorded along with the electrophysiological data. Finally, the datasets provide a complete set of metadata structured in a standardized format. These metadata allow easy access to detailed information about the datasets such as the settings of the recording hardware, the array specifications, the location of the implant in the motor cortex, information about the monkeys, or the offline spike sorting.
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-The two datasets can be exploited to address crucial issues in neurophysiology such as: What are the principles of neural interactions in a local cortical network and how are these interactions modulated during a well-described behavioral task? How different neuronal signals such as single-unit activity, multi-unit activity or LFPs relate to each other? Which spike sorting methods provide the best estimate of single unit activity?
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-We provide a dataset of microelectrode array recordings (MEA) from human pluripotent stem cell (hPSC)-derived and rat embryonic cortical neurons during their in vitro maturation ([Kapucu et al., to be published 2021](http://doi.org/to-be-inserted-after-publication)).
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-Data is prepared to assess extracellularly recorded spontaneous activity and compare the functional development of these neuronal networks.
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-With the evaluate spontaneous... development , response to pharmacological treatment..
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-In addition to the recordings of the spontaneous activity, we provide pharmacological responses of hPSC-derived and rat cortical cultures at their matured stage.
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-Together with the recorded electrode raw data, we also share the analysis code to form a comprehensive dataset including spike times, spike waveforms, burst activity and network synchronization metrics, which are calculated with two different connectivity estimators.
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-Moreover, we provide analysis code that produces the key scientific findings published previously with this dataset. ([Hyvärinen et al., 2019](https://doi.org/10.1038/s41598-019-53647-8))
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-This large dataset enables investigations of functional aspects of maturing cortical neuronal networks and provides substantial parameters to assess the differences and similarities between hPSC-derived and rat cortical networks in vitro.
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-This publicly available dataset will be beneficial to the experimental and computational neuroscientists .
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-PCA analysis to reveal the distinction between rat and human cell activity features
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-the accurate detailed description of data is delivered in the corresponding publication, data table code instructions
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-## Downloading the data
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-there are several ways to upload the data using GIN command line client, git annex and web browser. Short instructions for web browser and GIN CLI are described below.
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-### Web browser
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-The clear way to get a particular file from the repositorye using the web interface is to proceed to its folder, click the file and then click the "Download" link below it. The files containing raw MEA signals are quite large, so the downloading time may be extensive in case of slow Internet connection. The robustness of the connection is important as it happes so that browsers sometimes can not continue the file downloading after abrupt connection loss.
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-### GIN CLI
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-Create an account on GIN and download the GIN client [(instructions)](https://gin.g-node.org/G-Node/Info/wiki/GIN+CLI+Usage+Tutorial). Log in using CLI:
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-```bash
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-gin login
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-```
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-Clone the repository:
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-```bash
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-gin get AndreyVinogradov/attempt2
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-```
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-Big data files are not downloaded automatically. The following command should be used to get their contents:
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-```bash
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-gin get-content <filename>
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-```
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-Downloaded big files will be locked. You have to unlock the file with the following command:
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-```bash
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-gin unlock <filename>
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-```
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-To remove the contents of a big file:
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-```bash
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-gin lock <filename>
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-gin remove-content <filename>
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-```
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-Please, refer to the detailed GIN CLI [Usage Tutorial](https://gin.g-node.org/G-Node/Info/wiki/GIN+CLI+Usage+Tutorial).
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-Codes directory contains:
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-MATLAB spike detection
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-meaRtools analysis
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-Connectivity analysis
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-PCA analysis
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-each folder contain recording in hdf5 format (e.g. input for matlab spike detection)
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-Each .h5 file accomodate two groups: Data and DataInfo
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-Data group embeds a subgroup for each well of MEA plate. Each of these subgroups contains a number of datasets for each electrode in the well. For example, to access the recording of electode 11 of well A1 of ... .h5 recording the following command should be executed:
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-DataInfo group contains two datasets: and a list of attributes which together deliver the detailed description of ...
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-To load the dataset of excluded wells the following command should be exectuted:
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-The attribute reading command is a bit different:
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-folder with spike files (Matlab outputs) explog and noisy electrode files which together comprise meaRtools input.
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-and folder with selected meaRtools outputs
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-Pharmacology folders contain separate set folder for each stage of the pharmacological experiment (Baseline Pharmacology and TTX treatment). To check which well of MEA plate has undergone which specific treatment (e.g. drug or control) during Pharmacology and TTX stage it is recommended to take a glance into explog .csv file.
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-## Related Publications
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-* Kapucu, F.E., Vinogradov A., Hyvärinen T., Ylä-Outinen L., Narkilahti S. (2021, submitted, to be published soon). Comparative microelectrode array dataset of functional development of human PSC-derived and rat neuronal networks
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-* Hyvärinen, T., Hyysalo, A., Kapucu, F.E., Aarnos, L., Vinogradov, A., Eglen, J.E., Ylä-Outinen, L., Narkilahti, S. (2019). Functional characterization of human pluripotent stem cell-derived cortical networks differentiated on laminin-521 substrate: comparison to rat cortical cultures. Scientific Reports volume 9, 17125. https://doi.org/10.1038/s41598-019-53647-8
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-## Licensing
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-<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br /><span xmlns:dct="http://purl.org/dc/terms/" property="dct:title">
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-??????
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Andrey Vinogradov