 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 03, 2023 |
| Title |
Single nucleus gene expression profile of the rodent brains response to systemic innate immune system challenges |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The mammalian brain consists of heterogeneous cell populations with distinct responses to innate immune system challenges. Here we used single nucleus RNA sequencing (snRNAseq) to analyze cell type and stimulus dependent transcriptional responses of the rodent brain to peripheral LPS and Poly(I:C) challenges.
|
| |
|
| Overall design |
Innate immune system challenges were induced by the intra peritoneal (i.p.) application of lipopolysaccharide (LPS), polyinosinic:polycytidylic acid (poly(I:C)), or saline (sham control) treatment. Four animals were pooled per treatment-group, generating 3 single nucleus RNA sequenced (snRNAseq) datasets: Saline treated = RN_brain_Saline, LPS treated = RN_brain_LPS, Poly(I:C) treated = RN_brain_PIC. Seven hours after i.p. injection of LPS (5mg/kg bodyweight), poly(I:C) (12 mg/kg bodyweight), or saline brains were harvested for nuclei purification. Nuclei were isolated using nuclei extraction buffer (Miltenyi) and standard discontinuous iodixanol gradient separation, followed by library preparation using standard 10x Genomics workflows and snRNAseq (NovaSeq 6000, Illumina). Details on the study design and sample processing can be found in: Bormann, D., D. Copic, K. Klas, M. Direder, C. J. Riedl, G. Testa, H. Kühtreiber, E. Poreba, S. Hametner, B. Golabi, M. Salek, C. Haider, V. Endmayr, L. E. Shaw, R. Höftberger, H. J. Ankersmit and M. Mildner (2023). "Exploring the heterogeneous transcriptional response of the CNS to systemic LPS and Poly(I:C)." Neurobiology of Disease 188: 106339. https://doi.org/10.1016/j.nbd.2023.106339.
|
| Web link |
https://doi.org/10.1016/j.nbd.2023.106339
|
| |
|
| Contributor(s) |
Bormann D, Copic D, Klas K, Direder M, Riedl CJ, Testa G, Kühtreiber H, Poreba E, Hametner S, Golabi B, Salek M, Haider C, Endmayr V, Shaw LE, Höftberger R, Ankersmit HJ, Mildner M |
| Citation(s) |
37913832 |
| |
| Submission date |
Jun 29, 2023 |
| Last update date |
Nov 03, 2023 |
| Contact name |
Daniel Bormann |
| E-mail(s) |
daniel.bormann@meduniwien.ac.at
|
| Organization name |
Medical University of Vienna
|
| Department |
Department of Thoracic Surgery
|
| Lab |
Applied Immunology Laboratory
|
| Street address |
Waehringer Guertel 18-20
|
| City |
Vienna |
| State/province |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platforms (1) |
| GPL25947 |
Illumina NovaSeq 6000 (Rattus norvegicus) |
|
| Samples (3) |
|
| Relations |
| BioProject |
PRJNA989075 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE236114_RAW.tar |
151.2 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
