MERFISH Imaging of mesocorticolimbic regions in the mouse brain (Chronic saline for 7 Days + 3 Days withdrawal)
[ BIL ID: ace-dip-tub ]
Dataset Citation:
Zeng, Hongkui, Zeng, Hongkui, Kim, Dong-Wook, McMillen, Delissa, Martin, Naomi, Valera Cuevas, Nasmil, Olsen, Paul, Campos, Jazmin, Kunst, Michael, Ching, Lindsey, Wills, Lauren, Kelschenbach, Jennifer, Volsky, David, Kenny, Paul, O'Connor, Richard, Ishmam, Mohammad, Pillai, Piya, Shin, Miryung, Borjabad, Alejandra, Liu, Xiaokun, Kim, Mo-Jong, Chagtoo, Megha. (2023). MERFISH Imaging of mesocorticolimbic regions in the mouse brain (Chronic saline for 7 Days + 3 Days withdrawal) [Dataset/Microscopy]. Brain Image Library.
Abstract:
This dataset is generated by MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization) experiments with a 300 gene panel on whole brain coronal sections covering major mesocorticolimbic areas (e.g. PFC, ventral STR, TH, etc). Briefly, after classifying transcriptomic cell types from the MERFISH expression of cell type marker genes among 300 genes, we identified cell types showing differential expressions of cocaine-related genes in brain regions of interest.
Contributors and Roles:
Allen Institute ( ResearchGroup )
;
Zeng, Hongkui ( ProjectLeader ),
Allen Institute for Brain Science
;
Zeng, Hongkui ( ContactPerson ),
Allen Institute for Brain Science
;
Kim, Dong-Wook ( Researcher ),
Allen Institute for Brain Science
;
Waters, Jack ( Other ),
Allen Institute for Brain Science
;
McMillen, Delissa ( DataCollector ),
Allen Institute for Brain Science
;
Pagan, Chelsea ( ProjectManager ),
Allen Institute for Brain Science
;
Martin, Naomi ( DataCollector ),
Allen Institute for Brain Science
;
Valera Cuevas, Nasmil ( DataCollector ),
Allen Institute for Brain Science
;
Olsen, Paul ( DataCollector ),
Allen Institute for Brain Science
;
Campos, Jazmin ( DataCollector ),
Allen Institute for Brain Science
;
Kunst, Michael ( Researcher ),
Allen Institute for Brain Science
;
Ching, Lindsey ( Researcher ),
Allen Institute for Brain Science
;
Wills, Lauren ( Researcher ),
Icahn School of Medicine at Mount Sinai
;
Kelschenbach, Jennifer ( Researcher ),
Icahn School of Medicine at Mount Sinai
;
Volsky, David ( ProjectLeader ),
Icahn School of Medicine at Mount Sinai
;
Kenny, Paul ( ProjectLeader ),
Icahn School of Medicine at Mount Sinai
;
Icahn School of Medicine at Mount Sinai ( ResearchGroup )
;
O'Connor, Richard ( DataCollector ),
Icahn School of Medicine at Mount Sinai
;
Ishmam, Mohammad ( DataCollector ),
Icahn School of Medicine at Mount Sinai
;
Pillai, Piya ( DataCollector ),
Icahn School of Medicine at Mount Sinai
;
Shin, Miryung ( DataCollector ),
Icahn School of Medicine at Mount Sinai
;
Borjabad, Alejandra ( DataCollector ),
Icahn School of Medicine at Mount Sinai
;
Liu, Xiaokun ( DataCollector ),
Icahn School of Medicine at Mount Sinai
;
Kim, Mo-Jong ( DataCollector ),
Icahn School of Medicine at Mount Sinai
;
Chagtoo, Megha ( DataCollector ),
Icahn School of Medicine at Mount Sinai
Funding:
National Institutes of Health
( 5-U01-DA056003-02 ) Single cell transcriptomic and epigenomic changes during chronic HIV infection and cocaine self-administration
National Institutes of Health
( 5-U01-DA056003-02 ) Single cell transcriptomic and epigenomic changes during chronic HIV infection and cocaine self-administration
National Institutes of Health
( 5-U01-DA056003-02 ) Single cell transcriptomic and epigenomic changes during chronic HIV infection and cocaine self-administration
National Institutes of Health
( 5-U01-DA056003-02 ) Single cell transcriptomic and epigenomic changes during chronic HIV infection and cocaine self-administration
National Institutes of Health
( 5-U01-DA056003-02 ) Single cell transcriptomic and epigenomic changes during chronic HIV infection and cocaine self-administration
Technical Information:
spatial transcriptomics (Modality)
/ MERFISH (Technique)
Instrument Metadata
Specimen Metadata
| localid | 660396.0 |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 70.0 |
| ageunit | Days |
| sex | Male |
| genotype | Strain_Name='C57Bl/6J' |
| organlocalid | |
| organname | Brain |
| samplelocalid | 660396.0 |
| atlas | |
| locations | |
| linkage | [] |
Image Metadata
| xaxis | left-to-right |
| obliquexdim1 | |
| obliquexdim2 | |
| obliquexdim3 | |
| yaxis | left-to-right |
| obliqueydim1 | |
| obliqueydim2 | |
| obliqueydim3 | |
| zaxis | posterior-to-anterior |
| obliquezdim1 | |
| obliquezdim2 | |
| obliquezdim3 | |
| landmarkname | |
| landmarkx | |
| landmarky | |
| landmarkz | |
| number | NA |
| displaycolor | NA |
| representation | |
| flurophore | DAPI, NA |
| stepsizex | 0.108 |
| stepsizey | 0.108 |
| stepsizez | 1.5 |
| stepsizet | NA |
| channels | 3.0 |
| slices | 7.0 |
| z | 1.0 |
| xsize | |
| ysize | |
| zsize | |
| gbytes | |
| files | |
| dimensionorder | XYZ |
License:
Data:
Data location on the Brain Image Library Analysis Ecosystem:
/bil/data/63/05/63053886eb9f9771/660396
Dataset download link:
https://download.brainimagelibrary.org/63/05/63053886eb9f9771/660396
Metadata download link:
https://api.brainimagelibrary.org/retrieve?bildid=ace-dip-tub
Manifest download link:
/bil/pscstaff/icaoberg/bil-inventory/datasets/json/ace-dip-tub.json