MERSCOPE Imaging of WT, Trem2-R47H, 5xFAD and Trem2-R47H; 5xFAD samples
[ BIL ID: ace-ear-nap ]
Dataset Citation:
Xu, Xiangmin. (2024). MERSCOPE Imaging of WT, Trem2-R47H, 5xFAD and Trem2-R47H; 5xFAD samples [Dataset/Microscopy]. Brain Image Library.
Abstract:
This dataset contains MERSCOPE Imaging data of 19 coronal hemispheres in WT, Trem2-R47H, 5xFAD, and Trem2-R47H; 5xFAD mice. Sections were imaged with a 300 gene panel, combined with DAPI imaging for localization of cellular nuclei.
Methods:
A full protocol describing this work is available with the accompanying manuscript
Contributors and Roles:
Xu, Xiangmin ( ProjectLeader ),
University of California, Irvine
Funding:
National Institutes of Health
( 1-R01-AG082127-01 ) Single-cell transcriptomic and epigenomic analysis of brain cell vulnerabilities to tauopathies in early AD impacted brain regions
;
National Institutes of Health
( 1-U01-AG076791-01 ) Cell-type-specific neural circuit connectomes in the mouse models of aging and Alzheimer's disease
;
National Institutes of Health
( 1-R01-AG067153-01 ) Epigenomic analysis of neural circuits in Alzheimer's disease mouse models
;
National Institutes of Health
( 1-U54-AG054349-01 ) Bioinformatics and Data Management Core
;
National Institutes of Health
( 1-RF1-AG065675-01 ) Neural circuit mechanisms underlying AD-related memory impairments
Technical Information:
spatial transcriptomics (Modality)
/ MERFISH (Technique)
X-axis images are center to right orientation
Instrument Metadata
| microscopetype | MERSCOPE |
| microscopemanufacturerandmodel | Vizgen |
| objectivename | |
| objectiveimmersion | Oil |
| objectivena | |
| objectivemagnification | 60x |
| detectortype | |
| detectormodel | |
| illuminationtypes | |
| illuminationwavelength | 400–850 nm |
| detectionwavelength | |
| sampletemperature | Room Temperature |
Specimen Metadata
| localid | Kim_202201111602_20220111-WT-5xFAD10518pHip300GP_VMSC00101/region_1/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Female |
| genotype | Strain_Name='5xFAD', C57BL6 background |
| organlocalid | |
| organname | Brain |
| samplelocalid | 5xFAD1 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | Kim_202201111602_20220111-WT-5xFAD10518pHip300GP_VMSC00101/region_3/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Female |
| genotype | Strain_Name='5xFAD', C57BL6 background, technical replicate of Kim_202201111602_20220111-WT-5xFAD10518pHip300GP_VMSC00101/region_1/ |
| organlocalid | |
| organname | Brain |
| samplelocalid | 5xFAD2 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | 202209041036_20220904-5xFAD-TREM2-AnteHip-300x05_VMSC00101/region_3/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Male |
| genotype | Strain_Name='5xFAD', C57BL6 background |
| organlocalid | |
| organname | Brain |
| samplelocalid | 5xFAD3 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | 202204011403_20220401135320220401TREM5xADF12mo4hemip_VMSC00101/region_1/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Male |
| genotype | Strain_Name='5xFAD', C57BL6 background |
| organlocalid | |
| organname | Brain |
| samplelocalid | 5xFAD4 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | 202302031055_20230203TREM5xFAD-VZG171x04_VMSC05201/region_1/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Male |
| genotype | Strain_Name='5xFAD', C57BL6 background |
| organlocalid | |
| organname | Brain |
| samplelocalid | 5xFAD5 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | Kim2_202112171955_12172021TREM2-5x12Mo300GP_VMSC00101/region_1/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Male |
| genotype | Strain_Name='Trem2-R47H' |
| organlocalid | |
| organname | Brain |
| samplelocalid | Trem2_1 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | Kim2_202112171955_12172021TREM2-5x12Mo300GP_VMSC00101/region_2/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Male |
| genotype | Strain_Name='Trem2-R47H', technical replicate of Kim2_202112171955_12172021TREM2-5x12Mo300GP_VMSC00101/region_1/ |
| organlocalid | |
| organname | Brain |
| samplelocalid | Trem2_2 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | 202209041036_20220904-5xFAD-TREM2-AnteHip-300x05_VMSC00101/region_2/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Male |
| genotype | Strain_Name='Trem2-R47H' |
| organlocalid | |
| organname | Brain |
| samplelocalid | Trem2_3 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | 202204011403_20220401135320220401TREM5xADF12mo4hemip_VMSC00101/region_2/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Male |
| genotype | Strain_Name='Trem2-R47H' |
| organlocalid | |
| organname | Brain |
| samplelocalid | Trem2_4 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | 202302031055_20230203TREM5xFAD-VZG171x04_VMSC05201/region_2/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Male |
| genotype | Strain_Name='Trem2-R47H' |
| organlocalid | |
| organname | Brain |
| samplelocalid | Trem2_5 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | Kim2_202112171955_12172021TREM2-5x12Mo300GP_VMSC00101/region_0/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Female |
| genotype | Strain_Name='Trem2-R47H; 5xFAD' |
| organlocalid | |
| organname | Brain |
| samplelocalid | Trem2_5xFAD1 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | Kim2_202112171955_12172021TREM2-5x12Mo300GP_VMSC00101/region_1/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Female |
| genotype | Strain_Name='Trem2-R47H; 5xFAD', technical replicate of Kim2_202112171955_12172021TREM2-5x12Mo300GP_VMSC00101/region_0/ |
| organlocalid | |
| organname | Brain |
| samplelocalid | Trem2_5xFAD2 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | 202209041036_20220904-5xFAD-TREM2-AnteHip-300x05_VMSC00101/region_0/' |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Male |
| genotype | Strain_Name='Trem2-R47H; 5xFAD' |
| organlocalid | |
| organname | Brain |
| samplelocalid | Trem2_5xFAD3 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | 202204011403_20220401135320220401TREM5xADF12mo4hemip_VMSC00101/region_0/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Male |
| genotype | Strain_Name='Trem2-R47H; 5xFAD' |
| organlocalid | |
| organname | Brain |
| samplelocalid | Trem2_5xFAD4 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | 202302031055_20230203TREM5xFAD-VZG171x04_VMSC05201/region_0/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Male |
| genotype | Strain_Name='Trem2-R47H; 5xFAD' |
| organlocalid | |
| organname | Brain |
| samplelocalid | Trem2_5xFAD5 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | Kim_202201111602_20220111-WT-5xFAD10518pHip300GP_VMSC00101/region_0/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Female |
| genotype | Strain_Name='C57BL6' |
| organlocalid | |
| organname | Brain |
| samplelocalid | WT1 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | Kim_202201111602_20220111-WT-5xFAD10518pHip300GP_VMSC00101/region_2/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Female |
| genotype | Strain_Name='C57BL6', technical replicate of Kim_202201111602_20220111-WT-5xFAD10518pHip300GP_VMSC00101/region_0/ |
| organlocalid | |
| organname | Brain |
| samplelocalid | WT2 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | 202209041036_20220904-5xFAD-TREM2-AnteHip-300x05_VMSC00101/region_1/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Male |
| genotype | Strain_Name='C57BL6' |
| organlocalid | |
| organname | Brain |
| samplelocalid | WT3 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
| localid | 202302031055_20230203TREM5xFAD-VZG171x04_VMSC05201/region_3/ |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 12.0 |
| ageunit | months |
| sex | Male |
| genotype | Strain_Name='C57BL6' |
| organlocalid | |
| organname | Brain |
| samplelocalid | WT5 |
| atlas | AllenMouseV3 |
| locations | Coronal Section |
| linkage | [] |
Image Metadata
| xaxis | NA |
| obliquexdim1 | |
| obliquexdim2 | |
| obliquexdim3 | |
| yaxis | inferior-to-superior |
| obliqueydim1 | |
| obliqueydim2 | |
| obliqueydim3 | |
| zaxis | anterior-to-posterior |
| obliquezdim1 | |
| obliquezdim2 | |
| obliquezdim3 | |
| landmarkname | |
| landmarkx | |
| landmarky | |
| landmarkz | |
| number | 1.0 |
| displaycolor | (0.0,0.0,1.0) |
| representation | |
| flurophore | DAPI |
| stepsizex | NA |
| stepsizey | NA |
| stepsizez | |
| stepsizet | |
| channels | 1.0 |
| slices | 1.0 |
| z | 1.0 |
| xsize | |
| ysize | |
| zsize | |
| gbytes | |
| files | |
| dimensionorder |
Cited By:
License:
Data:
Data location on the Brain Image Library Analysis Ecosystem:
/bil/data/b7/2f/b72faf9d87d7fc00
Dataset download link:
https://download.brainimagelibrary.org/b7/2f/b72faf9d87d7fc00
Metadata download link:
https://api.brainimagelibrary.org/retrieve?bildid=ace-ear-nap
Manifest download link:
/bil/pscstaff/icaoberg/bil-inventory/datasets/json/ace-ear-nap.json