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| Status |
Public on Feb 05, 2024 |
| Title |
Spatiotemporal Patterns of Gene Expression Around Implanted Silicon Electrode Arrays |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Objective. Intracortical brain interfaces are an ever evolving technology with growing potential for clinical and research applications. The chronic tissue response to these devices traditionally has been characterized by glial scarring, inflammation, oxidative stress, neuronal loss, and blood-brain barrier disruptions. The full complexity of the tissue response to implanted devices is still under investigation. Approach. In this study, we have utilized RNA-sequencing to identify the spatiotemporal gene expression patterns in interfacial (within 100 µm) and distal (500 µm from implant) brain tissue around implanted silicon microelectrode arrays. Naïve, unimplanted tissue served as a control. Main results. The data revealed significant overall differential expression (DE) in contrasts comparing interfacial tissue vs naïve (157 DE genes), interfacial vs distal (94 DE genes), and distal vs naïve tissues (21 DE genes). Our results captured previously characterized mechanisms of the foreign body response, such as astroglial encapsulation, as well as novel mechanisms which have not yet been characterized in the context of indwelling neurotechnologies. In particular, we have observed perturbations in multiple neuron-associated genes which potentially impact the intrinsic function and structure of neurons at the device interface. In addition to neuron-associated genes, the results presented in this study identified significant DE in genes which are associated with oligodendrocyte, microglia, and astrocyte involvement in the chronic tissue response. Significance. The results of this study increase the fundamental understanding of the complexity of tissue response in the brain and provide an expanded toolkit for future investigation into the bio-integration of implanted electronics with tissues in the central nervous system.
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| Overall design |
Comparative gene expression profiling of interfacial tissue (within100um of implant), distal tissue (500um from implant), and naïve tissue (no-implant) at 24hours, 1-week, and 6-weeks post-implantation of electrode.
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| Contributor(s) |
Thompson CH, Saxena A, Heelan N, Salatino J, Purcell EK |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jan 29, 2024 |
| Last update date |
Feb 05, 2024 |
| Contact name |
Erin K Purcell |
| E-mail(s) |
epurcell@msu.edu
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| Organization name |
MICHIGAN STATE UNIVERSITY
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| Department |
Biomedical Engineering
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| Street address |
775 WOODLOT DRIVE
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| City |
EAST LANSING |
| State/province |
MI |
| ZIP/Postal code |
48823 |
| Country |
USA |
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| Platforms (1) |
| GPL25947 |
Illumina NovaSeq 6000 (Rattus norvegicus) |
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| Samples (48)
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| GSM8042909 |
134203, 1, 24 Hours, 100um, rat25, Left Hemisphere |
| GSM8042910 |
134204, 1c, 24 Hours, 500um, rat25, Left Hemisphere |
| GSM8042911 |
134205, 2, 24 Hours, 100um, rat25, Right Hemisphere |
| GSM8042912 |
134206, 2c, 24 Hours, 500um, rat25, Right Hemisphere |
| GSM8042913 |
134207, 3, 24 Hours, 100um, rat29, Left Hemisphere |
| GSM8042914 |
134208, 3c, 24 Hours, 500um, rat29, Left Hemisphere |
| GSM8042915 |
134209, 4, 24 Hours, 100um rat29, Right Hemisphere |
| GSM8042916 |
134210, 4c, 24 Hours, 500um, rat29, Right Hemisphere |
| GSM8042917 |
134211, 5, 24 Hours, 100um, rat30, Left Hemisphere |
| GSM8042918 |
134212, 5c, 24 Hours, 500um, rat30, Left Hemisphere |
| GSM8042919 |
134213, 6, 24 Hours, 100um, rat30, Right Hemisphere |
| GSM8042920 |
134214, 6c, 24 Hours, 500um, rat30, Right Hemisphere |
| GSM8042921 |
134215, 7, 1 Week, 100um, rat9, Right Hemisphere |
| GSM8042922 |
134216, 7c, 1 Week, 500um, rat9, Right Hemisphere |
| GSM8042923 |
134217, 8, 1 Week, 100um, rat10, Right Hemisphere |
| GSM8042924 |
134218, 8c, 1 Week, 500um, rat10, Right Hemisphere |
| GSM8042925 |
134219, 9, 1 Week, 100um, rat20, Left Hemisphere |
| GSM8042926 |
134220, 9c, 1 Week, 500um, rat20, Left Hemisphere |
| GSM8042927 |
134221, 10, 1 Week, 100um, rat22, Right Hemisphere |
| GSM8042928 |
134222, 10c, 1 Week, 500um, rat22, Right Hemisphere |
| GSM8042929 |
134223, 11, 1 Week, 100um, rat23, Left Hemisphere |
| GSM8042930 |
134224, 11c, 1 Week, 500um, rat23, Left Hemisphere |
| GSM8042931 |
134225, 12, 1 Week, 100um, rat23, Right Hemisphere |
| GSM8042932 |
134226, 12c, 1 Week, 500um, rat23, Right Hemisphere |
| GSM8042933 |
134227, 13, 6 Weeks, 100um, rat2, Left Hemisphere |
| GSM8042934 |
134228, 13c, 6 Weeks, 500um, rat2, Left Hemisphere |
| GSM8042935 |
134229, 14, 6 Weeks, 100um, rat11, Left Hemisphere |
| GSM8042936 |
134230, 14c, 6 Weeks, 500um, rat11, Left Hemisphere |
| GSM8042937 |
134231, 16, 6 Weeks, 100um, rat17, Left Hemisphere |
| GSM8042938 |
134232, 16c, 6 Weeks, 500um, rat17, Left Hemisphere |
| GSM8042939 |
134233, 17, 6 Weeks, 100um, rat17, Right Hemisphere |
| GSM8042940 |
134234, 17c, 6 Weeks, 500um, rat17, Right Hemisphere |
| GSM8042941 |
134235, 18, 6 Weeks, 100um, rat19, Left Hemisphere |
| GSM8042942 |
134236, 18c, 6 Weeks, 500um, rat19, Left Hemisphere |
| GSM8042943 |
134237, 19, 6 Weeks, 100um, rat19, Right Hemisphere |
| GSM8042944 |
134238, 19c, 6 Weeks, 500um, rat19, Right Hemisphere |
| GSM8042945 |
833-1, n2-R, Naïve, 100um, ratn2, Right Hemisphere |
| GSM8042946 |
833-2, n2-Rc, Naïve, 500um, ratn2, Right Hemisphere |
| GSM8042947 |
833-3, n2-L, Naïve, 100um, ratn2, Left Hemisphere |
| GSM8042948 |
833-4, n2-Lc, Naïve, 500um, ratn2, Left Hemisphere |
| GSM8042949 |
833-5, n3-R, Naïve, 100um, ratn3, Right Hemisphere |
| GSM8042950 |
833-6, n3-Rc, Naive, 500um, ratn3, Right Hemisphere |
| GSM8042951 |
833-7, n3-L, Naïve, 100um, ratn3, Left Hemisphere |
| GSM8042952 |
833-8, n3-Lc, Naïve, 500um, ratn3, Left Hemisphere |
| GSM8042953 |
833-9, n5-R, Naïve, 100um, ratn5, Right Hemisphere |
| GSM8042954 |
833-10, n5-Rc, Naïve, 500um, ratn5, Right Hemisphere |
| GSM8042955 |
833-11, n5-L, Naïve, 100um, ratn5, Left Hemisphere |
| GSM8042956 |
833-12, n5-Lc, Naïve, 500um, ratn5, Left Hemisphere |
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| Relations |
| BioProject |
PRJNA1070633 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE254474_Naivecontrols_deseq2_raw_counts.txt.gz |
278.8 Kb |
(ftp)(http) |
TXT |
| GSE254474_RS1_near_far_deseq2_raw_counts.txt.gz |
685.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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