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| Status |
Public on Mar 26, 2024 |
| Title |
PFA 35595 | 011 | Full ROI |
| Sample type |
SRA |
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| Source name |
Brain - Hippocampus
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| Organism |
Macaca mulatta |
| Characteristics |
tissue: Brain - Hippocampus
treatment: Chronic SIV CL757 infection
panel: (v1.0) Human NGS Immune Cell Profiling Protein Core, (v1.0) Human NGS Glial Cell Subtyping Protein, (v1.0) Human NGS Autophagy Protein, (v1.0) Human NGS Parkinson's Pathology Protein, (v1.0) Human NGS Alzheimer's Pathology Extended Protein, (v1.0) Human NGS Alzheimer's Pathology Protein, (v1.0) Human NGS Cell Death Protein, (v1.0) Human NGS Neural Cell Typing Protein, (v1.0) Human NGS PI3K/AKT Signaling Protein, (v1.0) Human NGS Pan-Tumor Protein Module, (v1.0) Human NGS MAPK Signaling Protein, (v1.0) Human NGS Immune Cell Typing Protein Module, (v1.0) Human NGS Immune Activation Status Protein Module, (v1.1) Human NGS IO Drug Target Protein Module, (v1.1) Human NGS Myeloid Module
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| Treatment protocol |
Rhesus macaques were intravenously inoculated with SIVCL757
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| Growth protocol |
N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
5um sections were cut from Paraformaldehyde-Fixed Paraffin-Embedded slides. Samples were incubated with either DNA-oligo barcoded RNA-ISH probes or antibodies which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Spatial transcriptome sequencing libraries were prepared with Nanostring reagents according to manufacturer's specifications
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
FFPE Spatial Transcriptome sequencing
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| Data processing |
Raw sequencing data was processed using Nanostring's GeoMx DSP Control Center
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Library strategy: Spatial Transcriptomics
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| Submission date |
Mar 19, 2024 |
| Last update date |
Mar 26, 2024 |
| Contact name |
Sonny Ramirez Elizaldi |
| E-mail(s) |
Srelizaldi@ucdavis.edu
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| Organization name |
University of California Davis
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| Department |
Immunology
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| Lab |
Iyer Lab
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| Street address |
County Road 98 and, Hutchison Dr
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| City |
Woodland |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL27943 |
| Series (1) |
| GSE261969 |
Spatial transcriptomics of the Rhesus Macaque Hippocampus during homeostasis and chronic SIV CL757 infection |
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| Relations |
| BioSample |
SAMN40547823 |
| SRA |
SRX23995527 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8155322_DSP-1012500008171-H-A12.dcc.gz |
48.8 Kb |
(ftp)(http) |
DCC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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