Replication Data for: MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures

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Mierau, Susanna; Sit, Timothy; Feord, Rachael; Oluigbo, David, 2024, "Replication Data for: MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures", https://doi.org/10.7910/DVN/Z14LWA, Harvard Dataverse, V4, UNF:6:VewDL+MOwDEGVxCIpVSLtA== [fileUNF]

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Description	This collection includes MATLAB-based code, microelectrode array (MEA) data, and other resources to assist users with our computational tool, the MEA network analysis pipeline (MEA-NAP). Dataverse contents: 1. MEA-NAP.zip - The MATLAB-based code for MEA-NAP version 1.6.0 that was used for the analysis in Sit et al. (2024) Cell Reports Methods. MEA-NAP version 1.10.0 is also included, which was the latest version at the time of publication of Sit et al. (2024). For the most up-to-date version, please see https://github.com/SAND-Lab/MEA-NAP/ 2. MEA-NAP GUI Tutorial.mp4 - This tutorial related to MEA-NAP versions 1.6 and 1.7. A detailed video guide to using MEA-NAP for new users. Please see our Github for links to video updates on MEA-NAP on our Synaptic and Network Development (SAND) YouTube channel. 3. NGN2_20230208_Data - MEA recordings from NGN2 neuronal cultures and batch analysis file. This data relates to Figure 3 in Sit et al. (2024). These are example inputs to MEA-NAP. 4. NGN2_20230208_OutputData - The full output folder including Steps 1-5 is zipped to preserve the folder organization. Outputs from Steps 1 and 2 are available for download as individual files. ** When viewing "Files" below, we recommend you "Change View" to "Tree". (2024-01-16)
Subject	Medicine, Health and Life Sciences
Keyword	neuroscience, network neuroscience, functional connectivity, network topology, network dynamics, neuronal cultures, human cerebral organoids, NGN2 iPSC-derived cortical cultures
Related Publication	Timothy PH Sit ✝, Rachael C Feord ✝, Alexander WE Dunn, Jeremi Chabros, David Oluigbo, Hugo H Smith, Lance Burn, Elise Chang, Alessio Boschi, Yin Yuan, George M Gibbons, Mahsa Khayat-Khoei, Francesco De Angelis, Erik Hemberg, Martin Hemberg, Madeline Lancaster, Andras Lakatos, Stephen J Eglen, Ole Paulsen, Susanna B Mierau. (2024) MEA-NAP: A flexible network analysis pipeline for neuronal 2D and 3D organoid multielectrode recordings. Cell Reports Methods, 4, 100901, November 18, 2024. doi: https://doi.org/10.1016/j.crmeth.2024.100901 ✝ equal contributionpmid: 38370637
License/Data Use Agreement	CC0 1.0

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	1 to 10 of 173 Files	Original Format Archival Format (.tab)
	MEA-NAP GUI Tutorial v1.6.mp4 MPEG-4 Video - 1.3 GB Published Mar 2, 2024 55 Downloads MD5: 2e386feec1c91641e6278405bcccce95 This video tutorial will guide you through using the interactive GUI that MEA-NAP offers for MEA-NAP versions 1.6-1.7. The interactive GUI facilitates the process of adjusting parameters to your specific data, especially if you have limited or no background in MATLAB. Please see our Github site for links to video updates on later MEA-NAP versions.	Preview "MEA-NAP GUI Tutorial v1.6.mp4" Access File File Access Public Download Options MPEG-4 Video Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	MEA-NAP-main_v1.10.zip ZIP Archive - 37.2 MB Published Nov 7, 2024 20 Downloads MD5: f5c2271afa73f22ed4da1ba69f7c1e61 Most recent version of MEA-NAP (version 1.10.0) at time of publication of Sit et al. (2024) in Cell Reports Methods. Includes documentation.	Preview "MEA-NAP-main_v1.10.zip" Access File File Access Public Download Options ZIP Archive Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	MEA-NAP-main_v1.6.0.zip ZIP Archive - 20.7 MB Published Apr 3, 2024 26 Downloads MD5: 47d8771b3177ab0f64587012928dc09a MATLAB-based code for the Microelectrode Array Network Analysis Pipeline (MEA-NAP) version 1.6.0. Downloaded from Github on 04/03/2024. This version was used for the data analysis in Sit et al. (2024). For the most up-to-date version, please see: https://github.com/SAND-Lab/MEA-NAP/	Preview "MEA-NAP-main_v1.6.0.zip" Access File File Access Public Download Options ZIP Archive Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	NGN2_20230208_OutputData_Steps1-5.zip ZIP Archive - 19.7 GB Published Mar 2, 2024 57 Downloads MD5: 53b69a3c60f10aebc50f9809e0f49f67 This is the complete MEA-NAP output for the NGN2_20230208 dataset. This is zipped to preserve the nested file structure for Steps 1-5.	Preview "NGN2_20230208_OutputData_Steps1-5.zip" Access File File Access Public Download Options ZIP Archive Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	NGN2_20230208_batchanalysislist.csv NGN2_20230208_Data/Tabular Data - 2.3 KB Published Mar 2, 2024 95 Downloads 3 Variables, 60 Observations UNF:6:5DtRhAVmEK7ti1GZN3OcKw== Comma-separated values file used to run batch analysis for NGN2 20230208 dataset in MEA-NAP. To use in MEA-NAP, save as a .csv file (Harvard Dataverse changed file extension to .tab.)	Preview "NGN2_20230208_Data/NGN2_20230208_batchanalysislist.csv" Preview "NGN2_20230208_Data/NGN2_20230208_batchanalysislist.csv" Access File File Access Public Download Options Comma Separated Values (Original File Format) Tab-Delimited RData Download Metadata DDI Codebook v2 Data File Citation Download EndNote XML Download RIS Download BibTeX Explore Options Data Explorer v2
	NGN2_20230208_P1_DIV14_A2.mat NGN2_20230208_Data/Hierarchical Data Format - 890.6 MB Published Mar 2, 2024 47 Downloads MD5: 97ff90a2a569ac07729a8ce1eb9bde3b	Preview "NGN2_20230208_Data/NGN2_20230208_P1_DIV14_A2.mat" Access File File Access Public Download Options Hierarchical Data Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX Download Auxiliary Files XML from NetCDF/HDF5 (NcML) NcML (0.1)
	NGN2_20230208_P1_DIV14_A3.mat NGN2_20230208_Data/Hierarchical Data Format - 926.8 MB Published Mar 2, 2024 19 Downloads MD5: ef54963b3338f72c6fdbd5433e253226	Preview "NGN2_20230208_Data/NGN2_20230208_P1_DIV14_A3.mat" Access File File Access Public Download Options Hierarchical Data Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX Download Auxiliary Files XML from NetCDF/HDF5 (NcML) NcML (0.1)
	NGN2_20230208_P1_DIV14_B2.mat NGN2_20230208_Data/Hierarchical Data Format - 892.5 MB Published Mar 2, 2024 15 Downloads MD5: cd693da7f2def200c9ca8b79d0f645ac	Preview "NGN2_20230208_Data/NGN2_20230208_P1_DIV14_B2.mat" Access File File Access Public Download Options Hierarchical Data Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX Download Auxiliary Files XML from NetCDF/HDF5 (NcML) NcML (0.1)
	NGN2_20230208_P1_DIV21_A2.mat NGN2_20230208_Data/Hierarchical Data Format - 899.3 MB Published Mar 2, 2024 16 Downloads MD5: d0a861bf215c960c8b0522530b4bf647	Preview "NGN2_20230208_Data/NGN2_20230208_P1_DIV21_A2.mat" Access File File Access Public Download Options Hierarchical Data Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX Download Auxiliary Files XML from NetCDF/HDF5 (NcML) NcML (0.1)
	NGN2_20230208_P1_DIV21_A3.mat NGN2_20230208_Data/Hierarchical Data Format - 937.6 MB Published Mar 2, 2024 16 Downloads MD5: 93d33d18fd067549c3f94579985d95ab	Preview "NGN2_20230208_Data/NGN2_20230208_P1_DIV21_A3.mat" Access File File Access Public Download Options Hierarchical Data Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX Download Auxiliary Files XML from NetCDF/HDF5 (NcML) NcML (0.1)

Citation Metadata

Persistent Identifier	doi:10.7910/DVN/Z14LWA
Publication Date	2024-03-02
Title	Replication Data for: MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures
Alternative Title	Replication Data for: MEA-NAP: A flexible network analysis pipeline for neuronal 2D and 3D organoid multielectrode recordings
Author	Brigham & Women's Hospital & Harvard Medical School0000-0002-1220-6423 University College London0000-0003-1149-0466 University of Cambridge0000-0001-7801-8137 Oluigbo, DavidBrigham & Women's Hospital
Point of Contact	Use email button above to contact. Mierau, Susanna (Harvard University)
Description	This collection includes MATLAB-based code, microelectrode array (MEA) data, and other resources to assist users with our computational tool, the MEA network analysis pipeline (MEA-NAP). Dataverse contents: 1. MEA-NAP.zip - The MATLAB-based code for MEA-NAP version 1.6.0 that was used for the analysis in Sit et al. (2024) Cell Reports Methods. MEA-NAP version 1.10.0 is also included, which was the latest version at the time of publication of Sit et al. (2024). For the most up-to-date version, please see https://github.com/SAND-Lab/MEA-NAP/ 2. MEA-NAP GUI Tutorial.mp4 - This tutorial related to MEA-NAP versions 1.6 and 1.7. A detailed video guide to using MEA-NAP for new users. Please see our Github for links to video updates on MEA-NAP on our Synaptic and Network Development (SAND) YouTube channel. 3. NGN2_20230208_Data - MEA recordings from NGN2 neuronal cultures and batch analysis file. This data relates to Figure 3 in Sit et al. (2024). These are example inputs to MEA-NAP. 4. NGN2_20230208_OutputData - The full output folder including Steps 1-5 is zipped to preserve the folder organization. Outputs from Steps 1 and 2 are available for download as individual files. ** When viewing "Files" below, we recommend you "Change View" to "Tree". (2024-01-16)
Subject	Medicine, Health and Life Sciences
Keyword	neuroscience, network neuroscience, functional connectivity, network topology, network dynamics, neuronal cultures, human cerebral organoids, NGN2 iPSC-derived cortical cultures
Related Publication	Timothy PH Sit ✝, Rachael C Feord ✝, Alexander WE Dunn, Jeremi Chabros, David Oluigbo, Hugo H Smith, Lance Burn, Elise Chang, Alessio Boschi, Yin Yuan, George M Gibbons, Mahsa Khayat-Khoei, Francesco De Angelis, Erik Hemberg, Martin Hemberg, Madeline Lancaster, Andras Lakatos, Stephen J Eglen, Ole Paulsen, Susanna B Mierau. (2024) MEA-NAP: A flexible network analysis pipeline for neuronal 2D and 3D organoid multielectrode recordings. Cell Reports Methods, 4, 100901, November 18, 2024. doi: https://doi.org/10.1016/j.crmeth.2024.100901 ✝ equal contribution pmid 38370637 https://doi.org/10.1016/j.crmeth.2024.100901 Timothy PH Sit ✝, Rachael C Feord ✝, Alexander WE Dunn, Jeremi Chabros, David Oluigbo, Hugo H Smith, Lance Burn, Elise Chang, Alessio Boschi, Yin Yuan, George M Gibbons, Mahsa Khayat-Khoei, Francesco De Angelis, Erik Hemberg, Martin Hemberg, Madeline Lancaster, Andras Lakatos, Stephen J Eglen, Ole Paulsen, Susanna B Mierau. (2024) MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures. bioRxiv 2024.02.05.578738; doi: https://doi.org/10.1101/2024.02.05.578738 ✝ equal contribution pmid 38370637 https://doi.org/10.1101/2024.02.05.578738
Language	English
Contributor	Research Group: Synaptic and Network Development (SAND) Group
Depositor	Mierau, Susanna
Deposit Date	2024-01-16
Date of Collection	Start Date: 2023-02-08
Data Type	Microelectrode array (MEA) data in MATLAB (.mat) format; MEA-NAP Output folder with figures (.png and .svg) and tabular data (.csv); MEA-NAP MATLAB scripts including documentation; Video tutorial (.mp4) to assist new users with MEA-NAP
Series	NGN2 20230208 Dataset: This dataset includes 60 MEA recordings (~56 GB total) and the batch analysis comma separated values (.csv) file for using with MEA-NAP. NGN iPSC-derived cortical neurons were plated at 35,000 cells, restricted to the area of the MEA, on 6-well (64-channel MEA per well) CytoView MEA plates (Axion Biosystems, M384-tMEA-6W). Raw voltage time series data was acquired at 12.5 kHz using the Axis software (Axion Biosystems). Raw data was exported to MATLAB (.mat) using a custom MATLAB script (rawConvert.m) that includes publicly available MATLAB scripts from Axion for separating the 6 MEA recordings per multi-well plate into individual MEA recordings. The filenames include the experimental code (NGN2), date of culture initiation (2023-02-08), plate number (P), days-in-vitro (DIV) on day of recording, and well number (e.g., A1, A2). --------------------------------------------------------------------------------------------------- NGN2 20230208 MEA-NAP Output Folder: A sample Output Folder (~27 GB total) is provided for the NGN2 20230208 dataset. The Output Folder was generated by the MEA network analysis pipeline (MEA-NAP) and contains a nested set of figures and data in tabular format. Please see the MEA-NAP documentation for more information. --------------------------------------------------------------------------------------------------- MEA-NAP Source Code and Documentation: The MEA network analysis pipeline (MEA-NAP) is a streamlined diagnostic and analytic tool for cellular-scale network activity data obtained using microelectrode arrays. MEA-NAP provides a straight forward way for new and experienced MATLAB users to quickly compare spike detection methods, neuronal activity (including firing rate and burst detection), and functional connectivity (including network metrics from graph and control theory). MEA-NAP performs batch analysis of an experimental dataset (e.g., MEA recordings from wild-type and knock-out cultures at multiple developmental time points). MEA-NAP produces summary plots and performs statistics on these features and organizes the output figures in a convenient file structure. The version (1.5.0) of MEA-NAP used for analysis of the data is saved as a compressed file here and includes the documentation. The most up-to-date version is at our Github: https://github.com/SAND-Lab/MEA-NAP --------------------------------------------------------------------------------------------------- MEA-NAP GUI Tutorial: Video guide for new users to MEA-NAP. ---------------------------------------------------------------------------------------------------
Software	MEA-NAP, Version: 1.6.0

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